Molecular dynamics simulations of glycoclusters and glycodendrimers
- PMID: 12071231
- DOI: 10.1016/s1389-0352(01)00072-1
Molecular dynamics simulations of glycoclusters and glycodendrimers
Abstract
Protein-carbohydrate recognition plays a crucial role in a wide range of biological processes, required both for normal physiological functions and the onset of disease. Nature uses multivalency in carbohydrate-protein interactions as a strategy to overcome the low affinity found for singular binding of an individual saccharide epitope to a single carbohydrate recognition domain of a lectin. To mimic the complex multi-branched oligosaccharides found in glycoconjugates, which form the structural basis of multivalent carbohydrate-protein interactions, so-called glycoclusters and glycodendrimers have been designed to serve as high-affinity ligands of the respective receptor proteins. To allow a rational design of glycodendrimer-type molecules with regard to the receptor structures involved in carbohydrate recognition, a deeper knowledge of the dynamics of such molecules is desirable. Most glycodendrimers have to be considered highly flexible molecules with their conformational preferences most difficult to elucidate by experimental methods. Longtime molecular dynamics (MD) simulations with inclusion of explicit solvent molecules are suited to explore the conformational space accessible to glycodendrimers. Here, a detailed geometric and conformational analysis of 15 glycodendrimers and glycoclusters has been accomplished, which differ with regard to their core moieties, spacer characteristics and the type of terminal carbohydrate units. It is shown that the accessible conformational space depends strongly on the structural features of the core and spacer moieties and even on the type of terminating sugars. The obtained knowledge about possible spatial distributions of the sugar epitopes exposed on the investigated hyperbranched neoglycoconjugates is detailed for all examples and forms important information for the interpretation and prediction of affinity data, which can be deduced from biological testing of these multivalent neoglycoconjugates.
Similar articles
-
Glycodendrimers: novel glycotope isosteres unmasking sugar coding. case study with T-antigen markers from breast cancer MUC1 glycoprotein.J Biotechnol. 2002 May;90(3-4):291-309. doi: 10.1016/s1389-0352(01)00065-4. J Biotechnol. 2002. PMID: 12071230 Review.
-
Design and synthesis of glycodendrimers.J Biotechnol. 2002 May;90(3-4):231-55. doi: 10.1016/s1389-0352(01)00062-9. J Biotechnol. 2002. PMID: 12071227 Review.
-
Non-covalent polyvalent ligands by self-assembly of small glycodendrimers: a novel concept for the inhibition of polyvalent carbohydrate-protein interactions in vitro and in vivo.Chemistry. 2005 Dec 16;12(1):99-117. doi: 10.1002/chem.200500901. Chemistry. 2005. PMID: 16231293
-
Artificial metalloglycoclusters: compact saccharide shell to induce high lectin affinity as well as strong luminescence.Bioconjug Chem. 2003 Jul-Aug;14(4):728-37. doi: 10.1021/bc020026a. Bioconjug Chem. 2003. PMID: 12862425
-
Multivalent cyclooligosaccharides: versatile carbohydrate clusters with dual role as molecular receptors and lectin ligands.Chemistry. 2002 May 3;8(9):1982-90. doi: 10.1002/1521-3765(20020503)8:9<1982::AID-CHEM1982>3.0.CO;2-5. Chemistry. 2002. PMID: 11981882
Cited by
-
Synthesis of carbohydrate-scaffolded thymine glycoconjugates to organize multivalency.Beilstein J Org Chem. 2015 May 7;11:668-74. doi: 10.3762/bjoc.11.75. eCollection 2015. Beilstein J Org Chem. 2015. PMID: 26124869 Free PMC article.
-
Scaffold diversity for enhanced activity of glycosylated inhibitors of fungal adhesion.RSC Med Chem. 2020 Aug 17;11(12):1386-1401. doi: 10.1039/d0md00224k. eCollection 2020 Dec 17. RSC Med Chem. 2020. PMID: 34095846 Free PMC article.
-
Partially glycosylated dendrimers block MD-2 and prevent TLR4-MD-2-LPS complex mediated cytokine responses.PLoS Comput Biol. 2011 Jun;7(6):e1002095. doi: 10.1371/journal.pcbi.1002095. Epub 2011 Jun 30. PLoS Comput Biol. 2011. PMID: 21738462 Free PMC article.
-
Structural studies of biologically active glycosylated polyamidoamine (PAMAM) dendrimers.J Mol Model. 2011 Aug;17(8):2051-60. doi: 10.1007/s00894-010-0907-1. Epub 2010 Dec 15. J Mol Model. 2011. PMID: 21161557
Publication types
MeSH terms
Substances
LinkOut - more resources
Full Text Sources
Other Literature Sources