Prediction and analysis of antifreeze proteins

Ryosuke Miyata; Yoshitaka Moriwaki; Tohru Terada; Kentaro Shimizu

doi:10.1016/j.heliyon.2021.e07953

Prediction and analysis of antifreeze proteins

Heliyon. 2021 Sep 8;7(9):e07953. doi: 10.1016/j.heliyon.2021.e07953. eCollection 2021 Sep.

Authors

Ryosuke Miyata¹, Yoshitaka Moriwaki¹, Tohru Terada¹, Kentaro Shimizu¹

Affiliation

¹ Department of Biotechnology, The University of Tokyo, 1-1-1 yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan.

Abstract

Antifreeze proteins (AFPs) are proteins that protect cellular fluids and body fluids from freezing by inhibiting the nucleation and growth of ice crystals and preventing ice recrystallization, thereby contributing to the maintenance of life in living organisms. They exist in fish, insects, microorganisms, and fungi. However, the number of known AFPs is currently limited, and it is essential to construct a reliable dataset of AFPs and develop a bioinformatics tool to predict AFPs. In this work, we first collected AFPs sequences from UniProtKB considering the reliability of annotations and, based on these datasets, developed a prediction system using random forest. We achieved accuracies of 0.961 and 0.947 for non-redundant sequences with less than 90% and 30% identities and achieved the accuracy of 0.953 for representative sequences for each species. Using the ability of random forest, we identified the sequence features that contributed to the prediction. Some sequence features were common to AFPs from different species. These features include the Cys content, Ala-Ala content, Trp-Gly content, and the amino acids' distribution related to the disorder propensity. The computer program and the dataset developed in this work are available from the GitHub site: https://github.com/ryomiya/Prediction-and-analysis-of-antifreeze-proteins.

Keywords: Amino acids; Antifreeze proteins; Prediction; Protein sequences; Random forest.