NMR paper Preparation of Amyloid Fibrils for Magic-Angle Spinning Solid-State NMR Spectroscopy.

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[NMR paper] Preparation of Amyloid Fibrils for Magic-Angle Spinning Solid-State NMR Spectroscopy.

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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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10-12-2015, 01:04 AM

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Preparation of Amyloid Fibrils for Magic-Angle Spinning Solid-State NMR Spectroscopy.

Preparation of Amyloid Fibrils for Magic-Angle Spinning Solid-State NMR Spectroscopy.

Related Articles Preparation of Amyloid Fibrils for Magic-Angle Spinning Solid-State NMR Spectroscopy.

Methods Mol Biol. 2016;1345:173-83

Authors: Tuttle MD, Courtney JM, Barclay AM, Rienstra CM

Abstract
Solid-state NMR spectroscopy (SSNMR) is an established and invaluable tool for the study of amyloid fibril structure with atomic-level detail. Optimization of the homogeneity and concentration of fibrils enhances the resolution and sensitivity of SSNMR spectra. Here, we present a fibrillization and fibril processing protocol, starting from purified monomeric ?-synuclein, that enables the collection of high-resolution SSNMR spectra suitable for site-specific structural analysis. This protocol does not rely on any special features of ?-synuclein and should be generalizable to any other amyloid protein.

PMID: 26453212 [PubMed - in process]

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