NMR paper NMR characterization of theinteraction of GroEL with amyloid ? as a model ligand.

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[NMR paper] NMR characterization of theinteraction of GroEL with amyloid ? as a model ligand.

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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

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NMR sample preparation:

Protein disorder:

DisMeta

Protein solubility:

Isotope labeling:

Solid-state NMR:

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04-23-2013, 08:37 PM

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NMR characterization of theinteraction of GroEL with amyloid ? as a model ligand.

NMR characterization of theinteraction of GroEL with amyloid ? as a model ligand.

Related Articles NMR characterization of theinteraction of GroEL with amyloid ? as a model ligand.

FEBS Lett. 2013 Apr 18;

Authors: Yagi-Utsumi M, Kunihara T, Nakamura T, Uekusa Y, Makabe K, Kuwajima K, Kato K

Abstract
Here we report an NMR study on the substrate interaction modes of GroEL using amyloid?(A?) as a model ligand. We found that GroEL could suppress A?(1-40) amyloid formation by interacting with its two hydrophobic segments Leu17-Ala21 and Ala30-Val36, which involve key residues in fibril formation. The binding site of A?(1-40) wasmapped on a pair of ?-helices located in the GroEL apical domain. These resultsprovide insights intochaperonin recognition of amyloidogenic proteins of pathological interest. STRUCTURED SUMMARY OF PROTEIN INTERACTIONS: A?(1-40)andA?(1-40)bindbyfluorescence technology(View interaction) A?(1-40)andA?(1-40)bindbynuclear magnetic resonance(View interaction) GroELandA?(1-40)bindbynuclear magnetic resonance(View interaction).

PMID: 23603391 [PubMed - as supplied by publisher]

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