Introduction: Human Beta Defensin1 (HBD1) is a key tumor-suppressing protein expressed in epithelial tissues. Gene expression of this protein is generally stable but can change under inflammatory conditions. The beta-defensin family consists of three members. Beta-defensin 1 has a structure that includes a core of three beta strands connected in an anti-parallel arrangement by intramolecular disulfide bonds. An alpha helix located in the N-terminal region of this protein covers this core structure. Beta-defensin 1 contains conserved motifs (Gly-X-Cys) that likely play a vital role in its stability. The purpose of this study was to investigate the effect of cysteine 59 to alanine mutation on the structure and stability of the protein using in silico molecular dynamics simulation.
Methods: The three-dimensional structure of C59A mutant beta-defensin 1, which lacked the pro-peptide region (amino acids 22 through 32) and the signal peptide (from amino acid 1 to 21), was predicted by the AlphaFold tool. Crystal structure of the native protein are listed in the RCSB database (https://www.rcsb.org) under the entries 1E4S, 1IJV, and 1IJU, and among them, 1IJU was selected as the reference structure for this study. Next, a molecular dynamics simulation was performed using GROMACS software for the native and mutant proteins over the 50-nanosecond. Finally, the RMSD, RMSF, and radius of gyration indices were examined for both proteins.
Results: The results of this simulation were visualized as a graph using R software and indicated a stable RMSD, a general decrease in the radius of gyration, and an increase in the RMSF in several amino acids preceding the mutation target (cysteine 59) in the mutant protein compared to the native one. This provides valuable insights regarding the reduction of the stability of the protein after mutation and the significance of this amino acid in the HBD-1 protein structure.
Conclusion: According to the data obtained from this study, it can probably be concluded that these conserved motifs, and especially cysteine 59, play an essential role in the stability of this protein. It is also expected that mutation in this amino acid will disrupt the structure of this protein, impairing its function. Since this protein plays a tumor suppressor role in some cancers, its mutation may contribute to cancer progression. Further studies at improving the structure and function of this protein could lead to valuable discoveries in the field of cancer treatment.