NMR paper Predictive Atomic Resolution Descriptions of Intrinsically Disordered hTau40 and ?-Synuclein in Solution from NMR and Small Angle Scattering.

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[NMR paper] Predictive Atomic Resolution Descriptions of Intrinsically Disordered hTau40 and ?-Synuclein in Solution from NMR and Small Angle Scattering.

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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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12-24-2013, 01:04 PM

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Predictive Atomic Resolution Descriptions of Intrinsically Disordered hTau40 and ?-Synuclein in Solution from NMR and Small Angle Scattering.

Predictive Atomic Resolution Descriptions of Intrinsically Disordered hTau40 and ?-Synuclein in Solution from NMR and Small Angle Scattering.

Related Articles Predictive Atomic Resolution Descriptions of Intrinsically Disordered hTau40 and ?-Synuclein in Solution from NMR and Small Angle Scattering.

Structure. 2013 Dec 18;

Authors: Schwalbe M, Ozenne V, Bibow S, Jaremko M, Jaremko L, Gajda M, Jensen MR, Biernat J, Becker S, Mandelkow E, Zweckstetter M, Blackledge M

Abstract
The development of molecular descriptions of intrinsically disordered proteins (IDPs) is essential for elucidating conformational transitions that characterize common neurodegenerative disorders. We use nuclear magnetic resonance, small angle scattering, and molecular ensemble approaches to characterize the IDPs Tau and ?-synuclein. Ensemble descriptions of IDPs are highly underdetermined due to the inherently large number of degrees of conformational freedom compared with available experimental measurements. Using extensive cross-validation we show that five different types of independent experimental parameters are predicted more accurately by selected ensembles than by statistical coil descriptions. The improvement increases in regions whose local sampling deviates from statistical coil, validating the derived conformational description. Using these approaches we identify enhanced polyproline II sampling in aggregation-nucleation sites, supporting suggestions that this region of conformational space is important for aggregation.

PMID: 24361273 [PubMed - as supplied by publisher]

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