Mechanical Properties of Super-soft Biomolecular Systems: Application to Twenty Solvated Canonical Amino Acids

Abstract

Amino acids (AAs) are the basic building blocks of proteins and regulate the body's metabolism. The mechanical properties of proteins play an essential role in their functionalities in addition to their structure and dynamic properties. They are paramount in understanding the flexibility, rigidity, and ability to resist deformation. It is critical to investigate the mechanical properties of the twenty standard AAs that comprise the protein. Herein, we have developed a computational approach based on a detailed ab initio quantum mechanical method based on density functional theory that can calculate the mechanical properties of strategically designed models of solvated AAs. This de novo approach has been applied to twenty standard amino acids as the first step towards exploring the mechanical properties of super-soft biomolecular systems. The calculated properties include the Young's modulus, shear modulus, bulk modulus, and Poisson's ratio under different strains. We have identified AAs with relatively higher/lower compressibility, rigidity, flexibility, stretchability, and hardness based on their mechanical properties. Our findings are valuable as the starting point for future studies on large peptides or small proteins.