MuSCaKDE - Multi-Scale modeling of Carbamoylated collagen: Kernel Density Estimation applied from all atom to rigid body simulation

Collagen, one of the main proteins constituting the extracellular matrix, is a complex structure with many unresolved questions regarding its functional organization. The sheer scale of the collagen system presents significant challenges for in-depth study. On one end of the scale, its size renders accurate analysis difficult. On the other end, its microscopic scale makes it impossible to visualize the system as a whole. What’s more, collagen fibers change various pathophysiological processes. One such modification, carbamoylation, involves the irreversible binding of isocyanic acid to protein amino groups, particularly lysine residues. Carbamoylation is one of the markers of aging in collagen fibers.This article presents a multi-scale approach aimed at characterizing the properties of collagen I fibers in their carbamoylated state. Kernel Density Estimation and Rigid Body Dynamics methodologies are coupled and implemented to propose an original approach for representing the positions and volumes preferentially explored by groups of atoms within a molecule.