Combining DNP NMR with segmental and specific labeling to study a yeast prion protein strain that is not parallel in-register [Biophysics and Computational Biology]

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Combining DNP NMR with segmental and specific labeling to study a yeast prion protein strain that is not parallel in-register [Biophysics and Computational Biology]

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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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04-04-2017, 10:41 PM

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Combining DNP NMR with segmental and specific labeling to study a yeast prion protein strain that is not parallel in-register [Biophysics and Computational Biology]

Combining DNP NMR with segmental and specific labeling to study a yeast prion protein strain that is not parallel in-register [Biophysics and Computational Biology]

Kendra K. Frederick, Vladimir K. Michaelis, Marc A. Caporini, Loren B. Andreas, Galia T. Debelouchina, Robert G. Griffin, Susan Lindquist...
Date: 2017-04-04

The yeast prion protein Sup35NM is a self-propagating amyloid. Despite intense study, there is no consensus on the organization of monomers within Sup35NM fibrils. Some studies point to a ?-helical arrangement, whereas others suggest a parallel in-register organization. Intermolecular contacts are often determined by experiments that probe long-range heteronuclear contacts... Read More

PNAS:
Number: 14
Volume: 114

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