Journal of Biochemical Sciences

ABSTRACT

The formation of the three-dimensional (3D) protein structure depends essentially on the amino acid-amino acid (AA-AA) interaction networks. Structural and computational approaches have been developed to predict these amino acid networks. However, there is a pressing need to estimate these interaction networks based on more accurate approaches, such as quantum-mechanical calculations. In this context, we calculated a parameter known as amino acid bond pairs (AABP), which we successfully applied to a variety of biological systems. AABP is applied to biomolecular systems, including SARS-CoV-2 spike protein, and the interface between spike protein and angiotensin enzyme 2 (ACE2). This new concept can be applied to protein design, understanding the mutation process leading to vaccine development.

KEYWORDS

1. Amino acid interaction network
2. Protein structure
3. Biomolecular system
4. AA bond pair unit
5. DFT calculation