Probing water-accessibility in HET-s(218-289) amyloid fibrils by solid-state NMR.

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Probing water-accessibility in HET-s(218-289) amyloid fibrils by solid-state NMR.

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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:

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NOEs, other restraints:

Chemical shifts:

RDCs:

Pseudocontact shifts:

Protein geomtery:

SAVES2 or SAVES4

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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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11-26-2010, 05:32 PM

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Probing water-accessibility in HET-s(218-289) amyloid fibrils by solid-state NMR.

Probing water-accessibility in HET-s(218-289) amyloid fibrils by solid-state NMR.

Probing water-accessibility in HET-s(218-289) amyloid fibrils by solid-state NMR.

J Mol Biol. 2010 Nov 18;

Authors: Van Melckebeke H, Schanda P, Gath J, Wasmer C, Verel R, Lange A, Meier BH, Böckmann A

Despite its importance in the context of conformational diseases, structural information is still sparse for protein fibrils. Hydrogen/deuterium exchange measurements of backbone amides allow to identify hydrogen-bonding patterns and reveal pertinent information about the amyloid ?-sheet architecture. However, they provide only little information about the identity of residues exposed to solvent or which are buried inside the fibril core. NMR spectroscopy is a potent method to identify solvent accessible residues in proteins via the observation of polarization transfer between chemically exchanging sidechain protons and water protons. We show here that the combined use of highly deuterated samples and fast magic-angle spinning (MAS) greatly attenuates unwanted spin diffusion and allows identifying polarization exchange with the solvent in a site-specific manner. We apply this measurement protocol to HET-s(218-289) prion fibrils under different conditions, including measurements carried out at physiological pH, where the protofibrils assemble together into thicker fibrils and demonstrate that each protofibril of HET-s(218-289) is surrounded by water, excluding extended dry inter-fibril contacts. We also show that exchangeable side-chain protons inside the hydrophobic core of HET-s(218-289) do not exchange over time intervals of weeks to months. The experiments proposed in this study can provide insight into detailed structural features of amyloid fibrils in general.

PMID: 21094164 [PubMed - as supplied by publisher]

Source: PubMed

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