Exploration of Conformational Spaces of High-Mannose-Type Oligosaccharides by an NMR-Validated Simulation

Exploration of the conformational spaces of flexible biomacromolecules is essential for quantitatively understanding the energetics of their molecular recognition processes. We employed stable isotope‐ and lanthanide‐assisted NMR approaches in conjunction with replica‐exchange molecular dynamics (RE...

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Published inAngewandte Chemie (International ed.) Vol. 53; no. 41; pp. 10941 - 10944
Main Authors Yamaguchi, Takumi, Sakae, Yoshitake, Zhang, Ying, Yamamoto, Sayoko, Okamoto, Yuko, Kato, Koichi
Format Journal Article
LanguageEnglish
Published Weinheim WILEY-VCH Verlag 06.10.2014
WILEY‐VCH Verlag
Wiley Subscription Services, Inc
EditionInternational ed. in English
Subjects
Atomic structure
Branched
Carbohydrate Conformation
Dynamics
Exploration
lanthanides
Lanthanoid Series Elements - chemistry
Magnetic Resonance Spectroscopy
Mannose - chemistry
Molecular dynamics
Molecular Dynamics Simulation
Molecular structure
NMR spectroscopy
Nuclear magnetic resonance
Oligosaccharides
Oligosaccharides - chemistry
paramagnetic effects
Simulation
NMR spectroscopy
molecular dynamics
paramagnetic effects
oligosaccharides
lanthanides
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Summary:Exploration of the conformational spaces of flexible biomacromolecules is essential for quantitatively understanding the energetics of their molecular recognition processes. We employed stable isotope‐ and lanthanide‐assisted NMR approaches in conjunction with replica‐exchange molecular dynamics (REMD) simulations to obtain atomic descriptions of the conformational dynamics of high‐mannose‐type oligosaccharides, which harbor intracellular glycoprotein‐fate determinants in their triantennary structures. The experimentally validated REMD simulation provided quantitative views of the dynamic conformational ensembles of the complicated, branched oligosaccharides, and indicated significant expansion of the conformational space upon removal of a terminal mannose residue during the functional glycan‐processing pathway. Watch this space: Lanthanide‐ and isotope‐assisted NMR approaches combined with replica‐exchange molecular dynamics simulations have been used to describe the conformational dynamics of complicated, branched oligosaccharides. The experimentally validated simulation provided quantitative views of the dynamic conformational ensembles of oligosaccharides with triantennary structures.
Bibliography:ark:/67375/WNG-5336QXNW-J
We thank Dr. Yasunori Chiba and Dr. Toshihiko Kitajima (The National Institute of Advanced Industrial Science and Technology) for providing the engineered yeast cells, Dr. Takahisa Ikegami (Osaka University) for his help with the NMR measurements, and Yukiko Isono (IMS) for her help in the preparation of the oligosaccharides. The NMR analyses in this study were performed, in part, under the Cooperative Research Program of the Institute for Protein Research, Osaka University. This work was partly supported by the Nanotechnology Platform Program of MEXT (Japan), MEXT/JSPS Grants in Aid for Scientific Research (25102008, 25102009, 24249002, 26560451and 24750170), and the Okazaki ORION project.
MEXT (Japan)
Okazaki ORION project
ArticleID:ANIE201406145
istex:755501A7B47ABFD70AB5F3914275F28C4C03E319
MEXT/JSPS - No. 25102008; No. 25102009; No. 24249002; No. 26560451; No. 24750170
ObjectType-Article-1
SourceType-Scholarly Journals-1
ObjectType-Feature-2
content type line 23
ISSN:1433-7851
1521-3773
DOI:10.1002/anie.201406145