NMR paper Direct Evidence for Hydrogen Bonding Between Hydroxyl Groups in Glycans: A Combined NMR and Molecular Dynamics Study.

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[NMR paper] Direct Evidence for Hydrogen Bonding Between Hydroxyl Groups in Glycans: A Combined NMR and Molecular Dynamics Study.

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NMR processing:

MDD

NMR assignment:

Backbone:

Side-chains:

NOEs:

Structure from NMR restraints:

Ab initio:

Fragment-based:

Rosetta-NMR (Robetta)

Template-based:

GeNMR

I-TASSER

Refinement:

Amber

Structure from chemical shifts:

Fragment-based:

Homology-based:

Torsion angles from chemical shifts:

Preditor

TALOS

Promega- Proline

Secondary structure from chemical shifts:

CSI (via RCI server)

TALOS

MICS caps, β-turns

d2D

PECAN

Flexibility from chemical shifts:

RCI

Interactions from chemical shifts:

HADDOCK

Chemical shifts re-referencing:

NMR model quality:

NOEs, other restraints:

Chemical shifts:

RDCs:

Pseudocontact shifts:

Protein geomtery:

SAVES2 or SAVES4

Quality Control Check

NMR spectrum prediction:

FANDAS

MestReS

V-NMR

Flexibility from structure:

Backbone S2

Methyl S2

B-factor

Molecular dynamics:

Gromacs

Amber

Antechamber

Chemical shifts prediction:

From structure:

Shiftx2

Sparta+

Camshift

CH3shift- Methyl

ArShift- Aromatic

ShiftS

Proshift

PPM

CheShift-2- Cα

From sequence:

Shifty

Camcoil

Poulsen_rc_CS

Disordered proteins:

MAXOCC

Format conversion & validation:

CCPN

From NMR-STAR 3.1

Validate NMR-STAR 3.1

NMR sample preparation:

Protein disorder:

DisMeta

Protein solubility:

Isotope labeling:

Solid-state NMR:

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03-28-2013, 04:03 PM

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Direct Evidence for Hydrogen Bonding Between Hydroxyl Groups in Glycans: A Combined NMR and Molecular Dynamics Study.

Direct Evidence for Hydrogen Bonding Between Hydroxyl Groups in Glycans: A Combined NMR and Molecular Dynamics Study.

Related Articles Direct Evidence for Hydrogen Bonding Between Hydroxyl Groups in Glycans: A Combined NMR and Molecular Dynamics Study.

J Phys Chem B. 2013 Mar 26;

Authors: Battistel MD, Pendrill R, Widmalm G, Freedberg DI

Abstract
With this report we introduce the abundant hydroxyl groups of glycans as NMR handles and structural probes that expand the repertoire of tools for structure-function studies on glycans in solution. To this end we present the facile detection and assignment of hydroxyl groups in a wide range of sample concentrations (0.5 to 1700 mM) and temperatures, ranging from -5 to 25 °C. We then exploit this information to directly detect hydrogen bonds, well known for their importance for molecular structural determination through NMR. Via HSQC-TOCSY we were able to determine directionality of these hydrogen bonds. Furthermore, by means of Molecular Dynamics simulations in conjunction with NMR, we establish that one out of the three detected hydrogen bonds arises from inter-molecular interactions, which may shed light in glycan-glycan interaction and their recognition by proteins.

PMID: 23531151 [PubMed - as supplied by publisher]

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