NMR paper A solution NMR toolset to probe the molecular mechanisms of amyloid inhibitors.

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[NMR paper] A solution NMR toolset to probe the molecular mechanisms of amyloid inhibitors.

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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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05-22-2018, 08:59 PM

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A solution NMR toolset to probe the molecular mechanisms of amyloid inhibitors.

Related Articles A solution NMR toolset to probe the molecular mechanisms of amyloid inhibitors.

Chem Commun (Camb). 2018 May 03;54(37):4644-4652

Authors: Ahmed R, Melacini G

Abstract
The self-association of the amyloid beta (A?) peptide into toxic oligomers is implicated in the early events leading to Alzheimer's disease (AD). Blocking the formation of A? oligomers and their interactions with the extracellular and cellular environment through small molecules and biopharmaceuticals is therefore a promising preventive strategy for AD. However, given the heterogeneity and transient nature of the A? oligomeric species, detailed structural and kinetic characterizations of such oligomers and oligomer:inhibitor complexes have proven to be challenging. Here, we discuss recent advancements in solution NMR that have been instrumental in overcoming these limitations and we provide two representative examples of A? inhibitors from our work to demonstrate the applications of such experiments, i.e. EGCG and human serum albumin.

PMID: 29658548 [PubMed - indexed for MEDLINE]

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