Developing an interface to simply check protein mutations for protein engineering

Developing an interface to simply check protein mutations for protein engineering
Alireza Doustmohammadi,¹ Seyed Shahriar Arab,^2,*
1. M.Sc. student in Bioinformatics, Tarbiat Modares University
2. Assistant Professor at Tarbiat Modares University
Introduction: Protein engineering is a widespread approach in the branch of structural biology. It is useful to redesign proteins to improve its function; correct incorrect protein folding or increase protein resistance about some environmental factors such as temperature. The first problem in protein engineering pipeline is what residue/s should be mutated and what residues should be replaced. We can use bioinformatics tools to decrease the problem space. OSPREY is one of this software that can be used to check different mutations and check protein energy and choose best mutations to check them in molecular dynamic tools such as Gromacs. OSPREY time complexity is very lower than molecular dynamic programs and its results are reliable but it’s not user friendly and usage of it be difficult for biologists. We develop a user-friendly interface for OSPREY to check different mutations. This interface works in protein and protein-peptide mode. It can help biologists to check difference mutations without conflict with program complexity.
Methods: Our interface input file is a PDB file. We alert users to add hydrogens to the protein files before check mutations. Users write protein chain name and residue number and write some amino acids to replace. Users write these details for any residue number in one line. In protein-peptide mode, the user should define the beginning and end of protein and peptide sequences and write mutations such as protein mode. The software results will display in .text format and it includes mutations and their energies. This software developed with PHP language.
Results: This interface helps biologists to simply check different mutations on proteins or protein-peptide complexes and select the best mutations according to energies.
Conclusion: The usage of bioinformatics tools is very important in experimental problems such as protein engineering. It decrease the time and cost complexity of the problem but these tools usage is difficult for biologists. we develop an interface for OSPREY software to check different mutations without conflict with software complexities.
Keywords: protein, protein engineering, mutation, peptide design, protein- peptide interaction