Protein Catalysis Through Structural Dynamics: A Comprehensive Analysis of Energy Conversion in Enzymatic Systems and Its Computational Limitations
Sarfaraz K. Niazi
Abstract
This review investigates the novel idea that proteins catalyze chemical reactions through conformational changes driven by energy derived from their collisions with water molecules. Recent studies have suggested that proteins in solution undergo constant deformation due to collisions with water molecules, generating potential energy that can be harnessed for catalytic functions. We detail the existing evidence supporting this idea, including how structures in proteins such as α-helices and β-sheets facilitate energy conversion, how conformational changes can affect the ways in which substrates attach, and how reactions occur. Combining information from computer-based methods-such as molecular dynamics simulations and machine learning models (e.g., AlphaFold)-we suggest a more complete model for understanding how proteins function beyond simply looking at their fixed shapes. This emerging view has implications for drug design, enzyme engineering, and our fundamental understanding of biological catalysis.