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  1. Article ; Online: The Influences of Sulphation, Salt Type, and Salt Concentration on the Structural Heterogeneity of Glycosaminoglycans

    Suman Samantray / Olujide O. Olubiyi / Birgit Strodel

    International Journal of Molecular Sciences, Vol 22, Iss 11529, p

    2021  Volume 11529

    Abstract: 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 ... ...

    Abstract 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.
    Keywords glycosaminoglycans ; sulphation ; GAG–cation interactions ; conformational flexibility ; molecular dynamics simulations ; Biology (General) ; QH301-705.5 ; Chemistry ; QD1-999
    Subject code 540
    Language English
    Publishing date 2021-10-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Article ; Online: Molecular Dynamics Simulation of Protein Biosurfactants

    David L. Cheung / Suman Samantray

    Colloids and Interfaces, Vol 2, Iss 3, p

    2018  Volume 39

    Abstract: Surfaces and interfaces are ubiquitous in nature and are involved in many biological processes. Due to this, natural organisms have evolved a number of methods to control interfacial and surface properties. Many of these methods involve the use of ... ...

    Abstract Surfaces and interfaces are ubiquitous in nature and are involved in many biological processes. Due to this, natural organisms have evolved a number of methods to control interfacial and surface properties. Many of these methods involve the use of specialised protein biosurfactants, which due to the competing demands of high surface activity, biocompatibility, and low solution aggregation may take structures that differ from the traditional head–tail structure of small molecule surfactants. As well as their biological functions, these proteins have also attracted interest for industrial applications, in areas including food technology, surface modification, and drug delivery. To understand the biological functions and technological applications of protein biosurfactants, it is necessary to have a molecular level description of their behaviour, in particular at surfaces and interfaces, for which molecular simulation is well suited to investigate. In this review, we will give an overview of simulation studies of a number of examples of protein biosurfactants (hydrophobins, surfactin, and ranaspumin). We will also outline some of the key challenges and future directions for molecular simulation in the investigation of protein biosurfactants and how this can help guide future developments.
    Keywords biosurfactants ; molecular dynamics simulation ; protein structure ; interfacial science ; Chemistry ; QD1-999
    Subject code 612
    Language English
    Publishing date 2018-09-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

    More links

    Kategorien

    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

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