Volume 14, Issue 4 (2023)
JMBS 2023, 14(4): 55-68 |
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jafari S, Emamzadeh R, Nazari M, Ganjalikhany M R. In silico study of the structure of FK domain in follistatin-like protein 1. JMBS 2023; 14 (4) :55-68
URL: http://biot.modares.ac.ir/article-22-67544-en.html
URL: http://biot.modares.ac.ir/article-22-67544-en.html
1- PhD student in biochemistry, Department of Cell and Molecular Biology & Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
2- Associate Professor of Department of Cell and Molecular Biology & Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran. ,r.emamzadeh@sci.ui.ac.ir
3- Associate Professor of Endocrine Research Center, Institute of Endocrinology and Metabolism, Iran University of Medical Sciences, Tehran, Iran4 Associate Professor of Nanobiotechnology Research Center, Avicenna Research Institute, ACECR, Tehran, Iran
4- Department of Cell and Molecular Biology & Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
2- Associate Professor of Department of Cell and Molecular Biology & Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran. ,
3- Associate Professor of Endocrine Research Center, Institute of Endocrinology and Metabolism, Iran University of Medical Sciences, Tehran, Iran4 Associate Professor of Nanobiotechnology Research Center, Avicenna Research Institute, ACECR, Tehran, Iran
4- Department of Cell and Molecular Biology & Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
Abstract: (829 Views)
Aim: Follistatin-like protein 1 (FSTL1) is a secreted glycoprotein that plays an important role in regulating cell survival, proliferation, differentiation, migration, inflammation, and modulating the immune system. The FK domain in FSTL1 has 10 conserved cysteine residues that form 5 disulfide bonds. Despite extensive studies on the function of FSTL1, limited structural information is available about this biologically important molecule.
Materials and Methods:Using the SWISS-MODEL server and using the crystal structure of the FK domain of the mouse FSTL1 protein with the code (PDB: 6jzw) as a template, structural models of the FK domain of the human FSTL1 protein were prepared. In the next step, the resulting structures were checked using Swiss-PDB Viewer 4.10, Chimera 1.12 software, Ramachandaran diagram and PDBSUM server, in terms of the distance between two cysteine residues, the modeling error range, and the formation of disulfide bonds. Molecular dynamics simulations were performed using the AMBER software package with the ff14SB force field.
Results: The results showed that the FK domain without disulfide bond has root mean square deviations (RMSD) and root mean square fluctuations (RMSF), higher than the native FK domain. In addition, the radius of gyration in domain without disulfide bonds is significantly lower than that of native FK domain. The results show that the disulfide bonds of the FK domain play a role in the stability of the structural folding of the FK domain and the removal of these bonds increases the structural flexibility of this domain.
Materials and Methods:Using the SWISS-MODEL server and using the crystal structure of the FK domain of the mouse FSTL1 protein with the code (PDB: 6jzw) as a template, structural models of the FK domain of the human FSTL1 protein were prepared. In the next step, the resulting structures were checked using Swiss-PDB Viewer 4.10, Chimera 1.12 software, Ramachandaran diagram and PDBSUM server, in terms of the distance between two cysteine residues, the modeling error range, and the formation of disulfide bonds. Molecular dynamics simulations were performed using the AMBER software package with the ff14SB force field.
Results: The results showed that the FK domain without disulfide bond has root mean square deviations (RMSD) and root mean square fluctuations (RMSF), higher than the native FK domain. In addition, the radius of gyration in domain without disulfide bonds is significantly lower than that of native FK domain. The results show that the disulfide bonds of the FK domain play a role in the stability of the structural folding of the FK domain and the removal of these bonds increases the structural flexibility of this domain.
Article Type: Original Research |
Subject:
Bioinformatics
Received: 2023/02/15 | Accepted: 2023/07/16 | Published: 2024/06/16
Received: 2023/02/15 | Accepted: 2023/07/16 | Published: 2024/06/16
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