Effect of Ion and Binding Site on the Conformation of Chosen Glycosaminoglycans at the Albumin Surface

• Published in: Entropy (Basel, Switzerland) Switzerland), 2022-06, Vol.24 (6), p.811
• Main Authors: Sionkowski, Piotr, Bełdowski, Piotr, Kruszewska, Natalia, Weber, Piotr, Marciniak, Beata, Domino, Krzysztof
• Format: Article
• Language: English
• Subjects: Addition polymerization; Affinity; Amino acids; Binding sites; Boundary lubrication; Cartilage; Chondroitin sulfate; conformational entropy; Cooperation; dihedral angles; Divalent cations; Domains; Electrolytes; Entropy; frequency distribution; Glycosaminoglycans; Heparan sulfate; human serum albumin; hyaluronan; Hyaluronic acid; Ligands; Lubrication; Molecular docking; Molecular dynamics; Serum albumin; Simulation; Surface charge
• ISSN: 1099-4300; 1099-4300
• DOI: 10.3390/e24060811

Albumin is one of the major components of synovial fluid. Due to its negative surface charge, it plays an essential role in many physiological processes, including the ability to form molecular complexes. In addition, glycosaminoglycans such as hyaluronic acid and chondroitin sulfate are crucial components of synovial fluid involved in the boundary lubrication regime. This study presents the influence of Na+, Mg2+ and Ca2+ ions on human serum albumin–hyaluronan/chondroitin-6-sulfate interactions examined using molecular docking followed by molecular dynamics simulations. We analyze chosen glycosaminoglycans binding by employing a conformational entropy approach. In addition, several protein–polymer complexes have been studied to check how the binding site and presence of ions influence affinity. The presence of divalent cations contributes to the decrease of conformational entropy near carboxyl and sulfate groups. This observation can indicate the higher affinity between glycosaminoglycans and albumin. Moreover, domains IIIA and IIIB of albumin have the highest affinity as those are two domains that show a positive net charge that allows for binding with negatively charged glycosaminoglycans. Finally, in discussion, we suggest some research path to find particular features that would carry information about the dynamics of the particular type of polymers or ions.