Effect of solvent and ions on the structure and dynamics of a hyaluronan molecule

Kutálková, Eva; Hrnčiřík, Josef; Witasek, Roman; Ingr, Marek

doi:10.1016/j.carbpol.2020.115919

Cited by 16 publications

(24 citation statements)

References 30 publications

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“…Recently, the effect of sulfation and cations on the conformational properties of disaccharides of CS and HS was studied through atomistic MD simulations. , Different macroscopic hydrodynamic properties of more than a hundred residues-long heparin sulfate chain were estimated using coarse-grained simulations . Also, different long sequences such as nonsulfated conformational ensembles of 10- and 20-mers of GAG chains and a 48-monosaccharide HA oligomer with varying salt concentrations and temperature were also investigated using MD simulations.…”

Section: Introductionmentioning

confidence: 99%

Effect of Sulfation on the Conformational Dynamics of Dermatan Sulfate Glycosaminoglycan: A Gaussian Accelerated Molecular Dynamics Study

2022

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Glycosaminoglycans (GAGs) are anionic biopolymers present on cell surfaces as a part of proteoglycans. The biological activities of GAGs depend on the sulfation pattern. In our study, we have considered three octadecasaccharide dermatan sulfate (DS) chains with increasing order of sulfation ( dp 6s, dp 7s, and dp 12s) to illuminate the role of sulfation on the GAG units and its chain conformation through 10 μs-long Gaussian accelerated molecular dynamics simulations. DS is composed of repeating disaccharide units of iduronic acid (IdoA) and N-acetylgalactosamine (N-GalNAc). Here, N-GalNAc is linked to IdoA via β(1–4), while IdoA is linked to N-GalNAc through α(1–3). With the increase in sulfation, the DS structure becomes more rigid and linear, as is evident from the distribution of root-mean-square deviations (RMSDs) and end-to-end distances. The tetrasaccharide linker region of the main chain shows a rigid conformation in terms of the glycosidic linkage. We have observed that upon sulfation (i.e., dp 12s), the ring flip between two chair forms vanished for IdoA. The dynamic cross-correlation analysis reveals that the anticorrelation motions in dp 12s are reduced significantly compared to dp 6s or dp 7s. An increase in sulfation generates relatively more stable hydrogen-bond networks, including water bridging with the neighboring monosaccharides. Despite the favorable linear structures of the GAG chains, our study also predicts few significant bendings related to the different puckering states, which may play a notable role in the function of the DS. The relation between the global conformation with the micro-level parameters such as puckering and water-mediated hydrogen bonds shapes the overall conformational space of GAGs. Overall, atomistic details of the DS chain provided in this study will help understand their functional and mechanical roles, besides developing new biomaterials.

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Section: Introductionmentioning

confidence: 99%

Effect of Sulfation on the Conformational Dynamics of Dermatan Sulfate Glycosaminoglycan: A Gaussian Accelerated Molecular Dynamics Study

2022

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“…HA’s biocompatibility is because of its high structural homology with endogenous HA in humans [ 7 ]. When dissolved in aqueous solution, HA swells and the chains of HA entangle and become random coils, leading to its unique viscoelasticity [ 6 , 8 , 9 ]. Because of its advantageous characteristics, such as high water retention, high biocompatibility, and viscoelasticity [ 10 ], HA has a wide range of applications for medicine, aesthetic medicine, and cosmetics.…”

Section: Introductionmentioning

confidence: 99%

Applications of Hyaluronic Acid in Ophthalmology and Contact Lenses

et al. 2021

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Hyaluronic acid (HA) is a glycosaminoglycan that was first isolated and identified from the vitreous body of a bull’s eye. HA is ubiquitous in the soft connective tissues of animals and therefore has high tissue compatibility for use in medication. Because of HA’s biological safety and water retention properties, it has many ophthalmology-related applications, such as in intravitreal injection, dry eye treatment, and contact lenses. Due to its broad range of applications, the identification and quantification of HA is a critical topic. This review article discusses current methods for analyzing HA. Contact lenses have become a widely used medical device, with HA commonly used as an additive to their production material, surface coating, and multipurpose solution. HA molecules on contact lenses retain moisture and increase the wearer’s comfort. HA absorbed by contact lenses can also gradually release to the anterior segment of the eyes to treat dry eye. This review discusses applications of HA in ophthalmology.

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“…To characterize the GAGs’ behavior in biological processes, it is paramount to develop an understanding of which specific structural patterns they adopt under different physiological conditions and how they do so [ 24 , 25 ]. In our work, we provide crucial insight into the structure and dynamics of various GAGs using molecular dynamics (MD) simulations.…”

Section: Introductionmentioning

confidence: 99%

The Influences of Sulphation, Salt Type, and Salt Concentration on the Structural Heterogeneity of Glycosaminoglycans

Samantray

Olubiyi

Strodel

2021

IJMS

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The increasing recognition of the biochemical importance of glycosaminoglycans (GAGs) has in recent times made them the center of attention of recent research investigations. It became evident that subtle conformational factors play an important role in determining the relationship between the chemical composition of GAGs and their activity. Therefore, a thorough understanding of their structural flexibility is needed, which is addressed in this work by means of all-atom molecular dynamics (MD) simulations. Four major GAGs with different substitution patterns, namely hyaluronic acid as unsulphated GAG, heparan-6-sulphate, chondroitin-4-sulphate, and chondroitin-6-sulphate, were investigated to elucidate the influence of sulphation on the dynamical features of GAGs. Moreover, the effects of increasing NaCl and KCl concentrations were studied as well. Different structural parameters were determined from the MD simulations, in combination with a presentation of the free energy landscape of the GAG conformations, which allowed us to unravel the conformational fingerprints unique to each GAG. The largest effects on the GAG structures were found for sulphation at position 6, as well as binding of the metal ions in the absence of chloride ions to the carboxylate and sulphate groups, which both increase the GAG conformational flexibility.

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Effect of solvent and ions on the structure and dynamics of a hyaluronan molecule

Cited by 16 publications

References 30 publications

Effect of Sulfation on the Conformational Dynamics of Dermatan Sulfate Glycosaminoglycan: A Gaussian Accelerated Molecular Dynamics Study

Effect of Sulfation on the Conformational Dynamics of Dermatan Sulfate Glycosaminoglycan: A Gaussian Accelerated Molecular Dynamics Study

Applications of Hyaluronic Acid in Ophthalmology and Contact Lenses

The Influences of Sulphation, Salt Type, and Salt Concentration on the Structural Heterogeneity of Glycosaminoglycans

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