Insights on the conformational properties of hyaluronic acid by using NMR residual dipolar couplings and MD simulations

被引:24
作者
Gargiulo, Valentina [1 ]
Morando, Maria A. [2 ]
Silipo, Alba [1 ]
Nurisso, Alessandra [3 ,4 ]
Perez, Serge [5 ]
Imberty, Anne [3 ,4 ]
Javier Canada, F. [2 ]
Parrilli, Michelangelo [1 ]
Jimenez-Barbero, Jesus [2 ]
De Castro, Cristina [1 ]
机构
[1] Univ Naples Federico II, Dept Organ Chem & Biochem, I-80126 Naples, Italy
[2] CSIC, Ctr Invest Biol, Madrid 28040, Spain
[3] Grenoble Univ, CNRS, UPR5301, Ctr Rech Macromol Vegetales CERMAV, F-38041 Grenoble 9, France
[4] ICMG, CNRS, UPR5301, Ctr Rech Macromol Vegetales CERMAV, F-38041 Grenoble 9, France
[5] ESRF, F-38000 Grenoble, France
关键词
molecular dynamics; POLYS; RDC; three-folded helix; XCluster; OLIGOSACCHARIDES; BIOMOLECULES; ALIGNMENT; FRAGMENTS;
D O I
10.1093/glycob/cwq067
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
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.
引用
收藏
页码:1208 / 1216
页数:9
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