Computational driven molecular dynamics simulation of keratinocyte growth factor behavior at different pH conditions

Abstract

Abstract Chronic wounds with a long healing period are considered a worldwide problem. As an important player in the wound healing process, keratinocyte growth factor (KGF) is one of the most effective methods of wound treatment. To prevent the wounds from becoming chronic, effective treatments should be applied at the first steps of wound generation. However, the low stability of KGF at acidic pH conditions at the first stages of the wound prevents its application in wound treatment. Lack of knowledge of the KGF behavior at different pHs has made it difficult to design the pH stable variants of this protein. In this study, we tried to simulate the KGF behavior at different pH conditions using molecular dynamics. To do this, the protonation and deprotonation states of KGF at different pH(s) were analyzed with PROPKA webserver. Then, the PDB files generated at different pHs were subjected to the molecular dynamic simulation at temperatures 300, 400, and 500 K using GROMACS software. The conformational stability, residue flexibility, protein compactness, and hydrogen-bond analysis were performed at the atomic level. The results showed that by decreasing the total charge of the protein from 10 at neutral pH to 7 at alkaline pH (pH: 9.0) at 500K, the KGF stability was significantly increased. Furthermore, analysis of the solvent-accessible surface area (SASA) showed that the KGF SASA is decreased with reduced protein charge. Analysis of the intra-protein and protein-solvent hydrogen bonds (H-bonds) showed that not only the number of H-bonds at alkaline pHs are higher compared to the neutral and acidic pHs, but also, they did not significantly decrease with increasing temperature at alkaline pH(s). Our results showed that the presence of more positively charged residues and their repulsion makes the KGF an unstable protein. Therefore, it seems that targeted mutations to reduce protein charge can lead to increased stability of KGF.