ThermoSeek: An Integrated Web Resource for Sequence and Structural Analysis of Proteins from Thermophilic Species

Protein engineering is a critical area within biotechnology, with enhancing protein thermal stability posing a significant challenge. Proteins from organisms adapted to extreme temperatures, such as thermophiles and psychrophiles, exhibit remarkable thermal stability. Analyzing their amino acid sequences, three-dimensional structures, and key residues provides valuable insights into the mechanisms of thermal adaptation. Traditional sequence alignment methods are used to identify homologous proteins in thermophiles, while recent advancements in protein structure prediction, particularly with AlphaFold2, have enabled more effective homology searches based on three-dimensional structures. In response to these advancements, we developed ThermoSeek, a web-accessible database integrating protein sequences, predicted structures, and key residues from both thermophilic and psychrophilic organisms. ThermoSeek offers three primary search modes: motif search, sequence alignment, and fold search, allowing researchers to explore protein adaptation to different thermal environments. These modes enable comparisons of query proteins with thermally stable proteins from diverse thermal conditions, investigating sequence homology, local residue environments (motifs), and fold similarity. To demonstrate its utility, we conducted case studies using ThermoSeek to search for thermophilic homologs of the PETases enzyme. This resource provides a comprehensive platform for understanding protein adaptation mechanisms across varying thermal environments and for optimizing enzyme stability. The ThermoSeek web application is publicly available at https://protein.org.cn/thermoseek