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

Abstract

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.

Flocculation efficiency of phosphorylated hemoglobin on kaolin and hematite systems

“…Protein above the pI has a negative charge due to the carboxyl group on the protein chains 23 . Divalent cations such as Ca 2+ can easily bind to the carboxyl group on the protein surface, causing the negative charge to decrease 24 …”

Atomic-Resolution Experimental Structural Biology and Molecular Dynamics Simulations of Hyaluronan and Its Complexes

“…Of the two, Ca 2+ had the stronger stabilization effect, with a greater tendency to form cation-mediated bridges between hyaluronan and albumin, presumably because of the lower hydration of Ca 2+ relative to Mg 2+ [ 173 ]. The greater capacity of Ca 2+ to form ionic interactions with the two biomolecules as compared to either Na + or Mg 2+ has been corroborated by second set of independent simulations [ 174 ].…”

Dissipative, Entropy Production Systems across Condensed Matter and Interdisciplinary Classical vs. Quantum Physics

“…Another paper collected by the SI which refers to CL systems, “Effect of Ion and Binding Site on the Conformation of Chosen Glycosaminoglycans at the Albumin Surface” [ 5 ], tackles the problem of ion-involving conformation of biopolymers called glycosaminoglycans near certain biopolymeric surfaces. Because of its negative surface charge, albumin plays an essential role in many physiological processes, including the ability to form molecular complexes.…”

“…In turn, glycosaminoglycans such as hyaluronan and/or chondroitin sulfate are key ingredients of synovial fluid involved in the boundary lubrication regime of an articular cartilage. This study [ 5 ] uncovers an impact of relatively small ions (Na + , Mg 2+ and Ca 2+ ), on human serum albumin–hyaluronan/chondroitin-sulfate interactions examined by means of molecular docking followed by molecular dynamics simulations. A certain type of glycosaminoglycan binding is analyzed by using a conformational entropy approach, and several protein–polymer complexes are studied to inspect, specifically, how the binding site and presence of ions influence their affinity conditions.…”

“…To summarize, this SI has focused on relevant and fundamental issues of statistical classical/quantum physics (and related subdisciplines), pointing to maximum-entropy and entropy production (and/or the spread of information) principles experienced by the respective CL and QU systems in (non)equilibrium conditions. The studies [ 1 , 2 , 3 , 4 , 5 , 6 , 7 , 8 , 9 , 10 ] disclose both the theoretical depth as well as the practical usefulness of the applied CL and QU approaches.…”