Structural analysis, molecular dynamics simulation and thermodynamic modification of the antifreeze protein type IV mutant under subfreezing temperatures

Abstract

Abstract Antifreeze proteins (AFPs) are expressed by numerous organisms for their survivability in polar regions due to their special functions; ice recrystallization inhibition (IRI) and thermal hysteresis (TH). Nevertheless, the inherent employment of AFPs proves to be an expensive and difficult process because of their limited effectiveness. Hence, a newly designed AFP with enhanced efficiency becomes essential to meet the needs of industries and the healthcare sector. In this study initially, the modified helix afp1m from yeast (Glaciozyma antarctica) was incorporated into the multi-helices of AFPIV with a new linker to boost the stability of the newly designed AFPIV (AFP1m3). To examine the physical and chemical qualities as well as the structural attributes various tools including ExPASy Prot-Param, Pep-Wheel, SWISS-MODEL, and Phyre2 were employed. Ultimately, the assessment and evaluation of the models as well as the exploration modification in the AFP1m3 model and AFPIV were conducted thermodynamically at melting and freezing temperatures using molecular dynamics (MD) simulation. The structural analysis carried out through computer simulation and subsequent validation revealed that the AFP1m3 model demonstrated hydrophobic properties and existed in a fully helical configuration with an exceptional structural integrity. The results of MD simulation indicated that AFP1m3 exhibited superior ice interaction energy, measuring at -950 kcal/mol, and displayed enhanced stability with a hydrogen bond lifetime of 60 ns when compared to AFPIV. Examining the behavior of AFP1m3 thermodynamically at four different temperatures (273 K, 269 K, 263 K, and 253 K) discovered that AFP1m3 exhibited greater effectiveness in subzero circumstances due to the hydrophobic and hydrophilic interactions, contrasting with AFPIV. This research provides a glimpse into the newly developed AFPIV, which exhibits remarkable effectiveness and shows substantial promise for utilization in diverse fields.