Effect of the radiation on amino acid based biomolecules via molecular dynamics simulation

Although amino acids, which are the building blocks of living organisms, take place in their lives and organisms, their function and effect have still not been determined. In addition, studies at the molecular level focus on proteins to determine the effects of radiation on living organisms. Molecular dynamics simulation has been used in this thesis study in order to examine the thermodynamic properties of proteins and the structural changes that radiation will create on proteins, with the simulation study to be performed at the atomic level, which cannot be studied with the experimental method. Analyzes has been made by examining the thermodynamic properties of proteins and the structural changes caused by temperature and ultraviolet radiation. Model structures were created for 25 biomolecules with different atomic numbers using CHARMM parameters with the Molecular Mechanical force field method, and simulations were made for these structures using the LAMMPS molecular dynamics simulator. The thermodynamic properties of 17 amino acids were determined by the simulations and the obtained parameters were compared with the experimental parameters. Calculations results is introduced that it is a difference of 2.57% between the simulation results and the experimental parameters. The thermodynamic properties of deca-alanine and one of the cell-penetrating peptides and the structural changes induced by radiation have been investigated. Thermodynamic properties related to temperature and structural changes caused by radiation have been investigated for the protein structure of human hemoglobin. Temperature-dependent thermodynamic properties have investigated for 2019-nCoV protease proteins and the thermodynamic properties for the 2019-nCoV spike protein structure were examined and the structural changes induced by radiation to the spike protein were analyzed.