Towards structure determination of self-assembled peptides using dynamic nuclear polarization enhanced solid-state NMR spectroscopy

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Towards structure determination of self-assembled peptides using dynamic nuclear polarization enhanced 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

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FANDAS

MestReS

V-NMR

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Backbone S2

Methyl S2

B-factor

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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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04-23-2014, 06:31 PM

nmrlearner

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Towards structure determination of self-assembled peptides using dynamic nuclear polarization enhanced solid-state NMR spectroscopy

From The DNP-NMR Blog:

Towards structure determination of self-assembled peptides using dynamic nuclear polarization enhanced solid-state NMR spectroscopy

Takahashi, H., et al., Towards structure determination of self-assembled peptides using dynamic nuclear polarization enhanced solid-state NMR spectroscopy. Angew Chem Int Ed Engl, 2013. 52(27): p. 6979-82.

http://www.ncbi.nlm.nih.gov/pubmed/23564735

Bio-inspired self-assemblies made of peptide building blocks have great potential for nanotechnology ranging from biological and pharmaceutical applications to (opto)electronics. With these goals, a variety of peptide nanoassemblies have been studied and designed over the last few decades. Inevitably, structural studies at an atomic scale are crucial to unravel the mechanisms that drive nanoassembly formation as well as to relate these structures to their physical and chemical properties. However, structure determination at an atomic level is challenging essentially because of the difficulty associated with using X-ray crystallography on such nanoassemblies.

Go to The DNP-NMR Blog for more info.

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