Publications Repository - Gdańsk University of Technology

The physicochemical basis of lubrication of articular cartilage is still not fully understood. However, the synergy between components of the synovial fluid can be a crucial factor that could explain this phenomenon. This work presents a nonlinear data analysis technique named the recurrence method, applied to the system involving two components of synovial fluid: albumin and chondroitin sulfate (CS) immersed in a water environment. This analysis is performed in order to obtain the ”statistical fingerprint” of the dynamics of the interaction between the molecules and to answer whether the variables are more deterministic or more random. The system simulation has been prepared by molecular docking method followed by molecular dynamics simulations. The already mentioned recurrence method has been applied to the time series of the energy of binding, and the time series of the number of intermolecular hydrogen bonds, as these features describe well binding between the two molecules. In detail, the time delay approach and embedded dimension approach have been applied to extract meaningful records from time series. Then, by means of recurrence plots and entropy approach, we discuss the similarities and differences between the molecular systems consisting of CS-4 and CS-6 molecules. Our main finding is a higher affinity of chondroitin sulfate IV to albumin as compared with chondroitin sulfate VI.

Authors

• Piotr Bełdowski,
• dr Piotr Weber link open in new tab ,
• Adam Gadomski,
• Piotr Sionkowski,
• Natalia Kruszewska,
• Krzysztof Domino