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Updated: Apr 17, 2026
Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
Published on: July 8, 2025
Protein evolution analysis of S-hydroxynitrile lyase by complete sequence design utilizing the INTMSAlign software.
Shogo Nakano1, Yasuhisa Asano1
11] Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan [2] Asano Active Enzyme Molecule Project, ERATO, JST, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan.
We developed INTMSAlign software to design functional proteins and predict protein evolution. This tool successfully created novel S-selective hydroxynitrile lyase (S-HNL) proteins, aiding studies in protein engineering and evolution.
Area of Science:
- Protein engineering
- Computational biology
- Biochemistry
Background:
- Designing functional proteins is crucial for advancing protein engineering and evolution studies.
- Existing methods may lack the precision for complete sequence design and evolutionary prediction.
Purpose of the Study:
- To develop and validate the INTMSAlign software for designing complete protein sequences.
- To apply the software to create novel functional proteins and analyze their evolutionary pathways.
Main Methods:
- Development of the INTMSAlign software for identifying consensus and correlation residues.
- Design and synthesis of three novel S-selective hydroxynitrile lyase (S-HNL) variants.
- Biochemical and sequence analysis of designed proteins and comparison with native S-HNL.
Main Results:
- The INTMSAlign software successfully designed functional S-HNL proteins with efficient folding.
- Designed S-HNLs exhibited characteristics suggesting neutral mutations accumulate during evolution from low to high activity.
- The study demonstrates the software's utility in protein sequence design and evolutionary prediction.
Conclusions:
- INTMSAlign software enables the design of complete functional protein sequences.
- The developed methods aid in predicting protein evolution, particularly within esterase and S-HNL families.
- This work contributes to both protein engineering and understanding evolutionary processes.
