Towards a Better Understanding of the Influence of Carbohydrates on the Structural, Dynamic, and Functional Properties of Fibromodulin: Crucial Insights From a Comparative In Silico Approach

ABSTRACT Proteoglycans are a class of biological macromolecules that are characterized by the presence of long chains of negatively charged glycosaminoglycans (GAGs). One family of proteoglycans, the small leucine‐rich proteoglycans (SLRPs), is a class of well‐conserved proteins, which are predominantly present in the extracellular matrix and are critical components of numerous processes in the extracellular matrix. Interestingly, fibromodulin (FMOD), one of the members of the SLRP family exists both as a proteoglycan and as a glycoprotein in juveniles and old‐aged individuals, respectively. Despite their physiological significance and interesting variations in their carbohydrate composition, their structural dynamics (e.g., evolution of their structure over time), and their 3D conformational preferences remains unexplored to date. In this study, molecular modeling techniques were used to investigate the effects of changes in carbohydrate composition on fibromodulin structure and dynamics. A total of 6µs of all‐atom molecular dynamics simulations were performed on three types of fibromodulin systems: non‐glycosylated FMOD, the glycoprotein form lacking charged keratan sulfate disaccharides and fibromodulin proteoglycan with keratan sulfate GAGs. Substantial changes were found in FMOD dynamics between the three states. These changes were accompanied by modifications to the curved‐solenoid architecture of FMOD, as well as local changes in solvent accessibilities to some critical residues. A relatively rigid, negatively charged motif, with a well‐conserved sequence across various FMOD species, was identified in the unstructured N‐terminal domain. This motif was highly accessible in both the proteoglycan and glycoprotein states, despite its proximity to carbohydrate chains. These two features (rigididy and high accessibility) suggest a key role for this motif in the protein‐protein interactions established by Fibromodulin. Overall, the study provides insight into how carbohydrate composition influences protein dynamics and functions.