Unraveling Protein Dynamics in the Presence of Cellulose Nanocrystals: An Essential ۱Dynamics Analysis

The dynamic behavior of proteins is crucial for their function, stability, and interactions.Among the various methods for analyzing protein dynamics, essential dynamics (ED) stands out byidentifying the most relevant motions, characterized by their large amplitude, that contributesignificantly to the overall dynamics of the system. By applying principal component analysis (PCA)to the covariance matrix of atomic positions, ED can effectively extract these dominant modes offluctuation, correlation, and conformational change [۱]. Herein, molecular dynamics (MD) simulationswere applied to investigate the essential dynamics of insulin in the presence of cellulose nanocrystals(CNC). A ۱۰۰۰-ns (۱-μs) MD simulation was conducted using the GROMACS package [۲]. To reducethe dimensionality of peptide dynamics, PCA was applied to the generated trajectories. The covariancematrix was constructed from atomic coordinates, and an eigenvalue decomposition was performedusing the Gmx covar and Gmx anaeig tools to obtain orthogonal collective modes. The results wereinterpreted by projecting displacement vectors onto PCA modes. The first ۲۵ PCs accounted for,respectively, ۵۵.۱%, ۳۴.۵%, and ۲۹.۷۳% of the total movements observed during the ۱-μs simulation.Our ED analysis revealed that the presence of CNC significantly influenced the peptide's dynamics.The collective modes identified through PCA revealed alterations in their amplitude and direction,suggesting that CNC-induced interactions modulated the peptide's conformational changes andfluctuation patterns. These findings provide valuable insights into the intricate interplay between insulinand CNC at the molecular level.

کلیدواژه ها:

Essential Dynamic ، Principal Component Analysis ، Covariance Matrix ، Peptide