Glycosaminoglycans (GAGs), long linear periodic anionic polysaccharides, are key molecules in the extracellular matrix (ECM). Therefore, deciphering their role in the biologically relevant context is important for fundamental understanding of the processes ongoing in ECM and for establishing new strategies in the regenerative medicine. Although GAGs represent a number of computational challenges, molecular docking is a powerful tool for analysis of their interactions. Despite the recent development of GAG‐specific docking approaches, there is plenty of room for improvement. Here, replica exchange molecular dynamics with repulsive scaling (REMD‐RS) recently proved to be a successful approach for protein–protein complexes, was applied to dock GAGs. In this method, effective pairwise radii are increased in different Hamiltonian replicas. REMD‐RS is shown to be an attractive alternative to classical docking approaches for GAGs. This work contributes to setting up of GAG‐specific computational protocols and provides new insights into the nature of these biological systems.

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The prediction power of computational methodologies for studying the role of ions in protein–glycosaminoglycan interactions was critically assessed.

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The binding interactions of bovine serum albumin (BSA) with tetraphenylborate ions ([B(Ph)4]−) have been investigated by a set of experimental methods (isothermal titration calorimetry, steady-state fluorescence spectroscopy, differential scanning calorimetry and circular dichroism spectroscopy) and molecular dynamics-based computational approaches. Two sets of structurally distinctive binding sites in BSA were found under the experimental conditions (10 mM cacodylate buffer, pH 7, 298.15 K). The obtained results, supported by the competitive interactions experiments of SDS with [B(Ph)4]− for BSA, enabled us to find the potential binding sites in BSA. The first site is located in the subdomain I A of the protein and binds two [B(Ph)4]− ions (logK(ITC)1 = 7.09 ± 0.10; ΔG(ITC)1 = −9.67 ± 0.14 kcal mol−1; ΔH(ITC)1 = −3.14 ± 0.12 kcal mol−1; TΔS(ITC)1 = −6.53 kcal mol−1), whereas the second site is localized in the subdomain III A and binds five ions (logK(ITC)2 = 5.39 ± 0.06; ΔG(ITC)2 = −7.35 ± 0.09 kcal mol−1; ΔH(ITC)2 = 4.00 ± 0.14 kcal mol−1; TΔS(ITC)2 = 11.3 kcal mol−1). The formation of the {[B(Ph)4]−}–BSA complex results in an increase in the thermal stability of the alfa-helical content, correlating with the saturation of the particular BSA binding sites, thus hindering its thermal unfolding.