The Application of i-Tasser and related studies to predict the full-length structure, thermodynamic states and functional analysis of the Kirsten Rat Sarcoma Virus (KRAS) protein; An observation of KRAS structural and functional integrity.

KRAS (Kirsten Rat Sarcoma Virus) is a Ras (Rat Sarcoma virus) family homologous. Due to its structural characteristics and biochemical properties, it’s been regarded as one of the most common drivers in various cellular signaling pathways. Due to its biochemical and pharmacological importance, KRAS been regarded as the “Holy Grail” of drug discovery. To understand the structure and thermodynamics of this protein, we tried to focus on the confirmational and functional portion of this specific protein. “i-Tesser” is applied to predict the structure of KRAS. A prediction for the secondary and full-length 3D structure been developed. Additional generation of the B factor value, Solvent accessibility, ligand bonded structure, as well as the 5 different thermodynamic state models of the KRAS and their functions are analyzed. The primary, metastable, ligand-bounded reactive states are visualized with the additional application of NAMD (Nanoscale Molecular Dynamics) and VMD (Visualization Molecular Dynamics). The drawn models showcase a C score value ranging between (-0.02 to -1.45) and Cluster density (0.0683 to 0.2835), along with a standard deviation value of (0.704983). Predicted secondary, 3D, and Thermodynamic models are drawn and supported by modeling their Solvent accessibility and B factor values. The 5 different models and the related structural and functional analysis provide additional information about the stability of KRAS structure and its function.