NMR paper Low-field and variable-field NMR relaxation studies of H2O and D2O molecular dynamics in articular cartilage

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[NMR paper] Low-field and variable-field NMR relaxation studies of H2O and D2O molecular dynamics in articular cartilage

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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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08-26-2021, 06:47 AM

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Low-field and variable-field NMR relaxation studies of H2O and D2O molecular dynamics in articular cartilage

Low-field and variable-field NMR relaxation studies of H2O and D2O molecular dynamics in articular cartilage

Osteoarthritis (OA) as the main degenerative disease of articular cartilage in joints is accompanied by structural and compositional changes in the tissue. Degeneration is a consequence of a reduction of the amount of macromolecules, the so-called proteoglycans, and of a corresponding increase in water content, both leading to structural weakening of cartilage. NMR investigations of cartilage generally address only the relaxation properties of water. In this study, two-dimensional (T1-T2)...

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