TITLE:
Applications of a Single Molecule Theory of Protein Dynamics
AUTHORS:
Yi Fang
KEYWORDS:
Folding, Denaturation, Binding, Post-Binding Deformation, Allostery, Dynamic Second Law of Thermodynamics
JOURNAL NAME:
Journal of Biosciences and Medicines,
Vol.12 No.6,
June
28,
2024
ABSTRACT: A single molecule theory for protein dynamics has been developed since 2012. It consists of the concepts of conformational Gibbs free energy function (CGF) and single molecule thermodynamic hypothesis (STH) that claims that all stable conformations are (local or global) minimizers of CGF. These are enough to give a unified explanations and mechanisms to many aspects of protein dynamics such as protein folding; allostery; denaturation; and intrinsically disordered proteins. Formulas of CGF in water environment had been derived via quantum statistics. Applications of them to soluble proteins are: docking Gibbs free energy difference formula and a practical way to search better docking site; single molecule binding affinity; predicting and explaining why structures of a monomeric globular protein looks like a globule and is tightly packed with a hydrophobic core; a representation of the hydrophobic effect; and a wholistic view to structures of water soluble proteins.