Design, modeling, docking and molecular dynamics simulation of a fusion peptide with the ability to bind to the growth factor of bone morphogenetic proteins.

Bahri, Mina; Hasannia, Sadegh; Shiri Hamedani, Alireza; Askari, Soudabeh

Design, modeling, docking and molecular dynamics simulation of a fusion peptide with the ability to bind to the growth factor of bone morphogenetic proteins.

Authors

Mina Bahri ¹

Sadegh Hasannia ²

Alireza Shiri hamedani ¹

Soudabeh Askari ³

¹ Department of academic affairs, Imam khomeini hospital complex, Tehran university of medical sciences, Tehran, Iran

² Department of biochemistry, Faculty of biological sciences, Tarbiat modares university, Tehran, Iran

³ Applied Razi Biotechnology, Kermanshah, Iran

Abstract

Today, the engineering of bone tissue has created special solutions to restore bone tissue by combining biological materials with a scaffold to provide cells suitable for bone formation and growth factors. In this research, a fusion peptide was designed with bioinformatics methods that can bind to the growth factors involved in bone tissue repair and lead to the trapping of these factors in the lesion site. In this study, heparin-binding domain was placed in the designed peptide and this peptide was complexed with growth factor in monomer and dimer forms with the help of docking. The structures of the complex were selected based on the lowest scores obtained, which included -912.5 and -1117, respectively. According to the results of docking and molecular dynamics simulation, this fusion peptide was able to bind to the growth factor of bone morphogenetic proteins. Based on the results of the simulation, unlike the peptide in the monomer state, the changes in the RMSD diagram of the peptide complex in the dimer state became stable after 10 nanoseconds from the simulation time and remained stable until the end of the simulation. These results show that the resulting complex in the dimer state has a better pattern of stability compared to the monomer state according to the investigation of the RMSD factor.

Keywords

Peptide fusion

Growth Factor

Docking

Molecular dynamics simulation

Heparin

Subjects

Bioinformatics

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