Enhancing Machine-Learning Prediction of Enzyme Catalytic Temperature Optima through Amino Acid Conservation Analysis

• Published in: International journal of molecular sciences Vol. 25; no. 11; p. 6252
• Main Authors: Cao, Yinyin, Qiu, Boyu, Ning, Xiao, Fan, Lin, Qin, Yanmei, Yu, Dong, Yang, Chunhe, Ma, Hongwu, Liao, Xiaoping, You, Chun
• Format: Journal Article
• Language: English
• Published: Basel MDPI AG 01.06.2024; MDPI
• Subjects: Amino acids; Artificial intelligence; conserved amino acids; Datasets; Enzymes; Machine learning; multiple sequence alignment; Normal distribution; optimal catalytic temperature; Phosphatase; Phosphatases; Product development; Proteins; Research methodology; Systems stability; Temperature; Weather forecasting; China
• ISSN: 1422-0067; 1661-6596; 1422-0067
• DOI: 10.3390/ijms25116252

Enzymes play a crucial role in various industrial production and pharmaceutical developments, serving as catalysts for numerous biochemical reactions. Determining the optimal catalytic temperature (T [sub.opt]) of enzymes is crucial for optimizing reaction conditions, enhancing catalytic efficiency, and accelerating the industrial processes. However, due to the limited availability of experimentally determined T [sub.opt] data and the insufficient accuracy of existing computational methods in predicting T [sub.opt], there is an urgent need for a computational approach to predict the T [sub.opt] values of enzymes accurately. In this study, using phosphatase (EC 3.1.3.X) as an example, we constructed a machine learning model utilizing amino acid frequency and protein molecular weight information as features and employing the K-nearest neighbors regression algorithm to predict the T [sub.opt] of enzymes. Usually, when conducting engineering for enzyme thermostability, researchers tend not to modify conserved amino acids. Therefore, we utilized this machine learning model to predict the T [sub.opt] of phosphatase sequences after removing conserved amino acids. We found that the predictive model’s mean coefficient of determination (R[sup.2]) value increased from 0.599 to 0.755 compared to the model based on the complete sequences. Subsequently, experimental validation on 10 phosphatase enzymes with undetermined optimal catalytic temperatures shows that the predicted values of most phosphatase enzymes based on the sequence without conservative amino acids are closer to the experimental optimal catalytic temperature values. This study lays the foundation for the rapid selection of enzymes suitable for industrial conditions.