NMR paper 2D solid state NMR spectral simulation of 3(10), alpha, and pi-helices.

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[NMR paper] 2D solid state NMR spectral simulation of 3(10), alpha, and pi-helices.

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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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11-24-2010, 09:51 PM

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2D solid state NMR spectral simulation of 3(10), alpha, and pi-helices.

2D solid state NMR spectral simulation of 3(10), alpha, and pi-helices.

Related Articles 2D solid state NMR spectral simulation of 3(10), alpha, and pi-helices.

J Magn Reson. 2004 Jun;168(2):187-93

Authors: Kim S, Cross TA

Transmembrane helices are more uniform in structure than similar helices in water soluble proteins. Solid state NMR of aligned bilayer samples is being increasingly used to characterize helical membrane protein structures. Traditional spectroscopic methods have difficulty distinguishing between helices with i to i + 3 (3(10)), i to i + 4 (alpha), and i to i + 5 (pi) hydrogen bonding topology. Here, we show that resonance patterns in PISEMA spectra simulated for these different helices show unique and striking features. The size and shape of these Polar Index Slant Angle (PISA) wheels, as well as the resonances per turn and clockwise versus counter-clockwise sequential connectivity of the resonances demonstrate how these different helical structures, if present as a uniform structure, will be readily distinguished, and characterized.

PMID: 15140426 [PubMed - indexed for MEDLINE]

Source: PubMed

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