Taxonomic group: bacteria / Firmicutes
(Phylum: Firmicutes)
NCBI PubMed ID: 20466653Journal NLM ID: 9104124Publisher: IRL Press at Oxford University Press
Correspondence: decastro
unina.it
Institutions: Department of Organic Chemistry and Biochemistry, University of Napoli Federico II, Complesso Universitario Monte Sant'Angelo, Via Cintia 4, Naples, Italy
The conformational features of hyaluronic acid, a key polysaccharide with important biological properties, have been determined through the combined used of nuclear magnetic resonance (NMR) spectroscopy and molecular modeling techniques. A decasaccharide fragment of sodium hyaluronate (HA) was submitted to 3.5 ns of molecular dynamics in explicit water environment form. The same decasaccharide was prepared by hyaluronidase digestion for the experimental study. The approach consisted in the measurements of NMR residual dipolar coupling (RDC) which were used to filter the molecular dynamics data by retaining those structures which were in agreement with the experimental observations. Further analysis of the new conformer ensemble (HA(RDC)) and clustering the molecules with respect to their overall length led to seven representative structures, which were described in terms of their secondary motifs, namely the best fitting helix geometry. As a result, this protocol permitted the assessment that hyaluronic acid can adopt two different arrangements, which can be described by a three- or four-folded left-handed helix, with a higher occurrence of the first one.
molecular, molecular dynamics, POLYS, RDC, three-foldedhelix, XCluster
Structure type: suggested polymer biological repeating unit ; 100000-10000000
Location inside paper: p.1208
Trivial name: hyaluronic acid
Compound class: EPS
Contained glycoepitopes: IEDB_115136,IEDB_135813,IEDB_137340,IEDB_140630,IEDB_141807,IEDB_151527,IEDB_151531,IEDB_231709,IEDB_423153
Methods: NMR-2D, MD simulations, NMR-1D, enzymatic digestion, RDC, computation with POLYS, superimposition analysis
Comments, role: polymerization frame was shifted to accord biological repeating unit in IDs 43173, 117092
3D data: molecular modeling
Related record ID(s): 25649
NCBI Taxonomy refs (TaxIDs): 1336Reference(s) to other database(s): GTC:G28158RP, GlycomeDB:
899
Show glycosyltransferases
There is only one chemically distinct structure:
Taxonomic group: bacteria / Firmicutes
(Phylum: Firmicutes)
NCBI PubMed ID: 20466653Journal NLM ID: 9104124Publisher: IRL Press at Oxford University Press
Correspondence: decastro
unina.it
Institutions: Department of Organic Chemistry and Biochemistry, University of Napoli Federico II, Complesso Universitario Monte Sant'Angelo, Via Cintia 4, Naples, Italy
The conformational features of hyaluronic acid, a key polysaccharide with important biological properties, have been determined through the combined used of nuclear magnetic resonance (NMR) spectroscopy and molecular modeling techniques. A decasaccharide fragment of sodium hyaluronate (HA) was submitted to 3.5 ns of molecular dynamics in explicit water environment form. The same decasaccharide was prepared by hyaluronidase digestion for the experimental study. The approach consisted in the measurements of NMR residual dipolar coupling (RDC) which were used to filter the molecular dynamics data by retaining those structures which were in agreement with the experimental observations. Further analysis of the new conformer ensemble (HA(RDC)) and clustering the molecules with respect to their overall length led to seven representative structures, which were described in terms of their secondary motifs, namely the best fitting helix geometry. As a result, this protocol permitted the assessment that hyaluronic acid can adopt two different arrangements, which can be described by a three- or four-folded left-handed helix, with a higher occurrence of the first one.
molecular, molecular dynamics, POLYS, RDC, three-foldedhelix, XCluster
Structure type: oligomer
Location inside paper: p.1208
Trivial name: hyaluronic acid
Contained glycoepitopes: IEDB_115136,IEDB_135813,IEDB_137340,IEDB_140630,IEDB_141807,IEDB_151527,IEDB_151531,IEDB_231709,IEDB_423153
Methods: NMR-2D, MD simulations, NMR-1D, enzymatic digestion, RDC, computation with POLYS, superimposition analysis
Enzymes that release or process the structure: bovine testicular hyaluronidase
Comments, role: HA decasaccharide after enzymatic depolymerization
3D data: molecular modeling
Related record ID(s): 25252
NCBI Taxonomy refs (TaxIDs): 1336Reference(s) to other database(s): GTC:G60511GB, GlycomeDB:
37861
Show glycosyltransferases
There is only one chemically distinct structure:
Found 
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