NMR paper Quantitative analysis of 1H NMR detected proteins in the rat cerebral cortex in vivo

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[NMR paper] Quantitative analysis of 1H NMR detected proteins in the rat cerebral cortex in vivo

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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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08-21-2010, 11:53 PM

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Quantitative analysis of 1H NMR detected proteins in the rat cerebral cortex in vivo

Quantitative analysis of 1H NMR detected proteins in the rat cerebral cortex in vivo and in vitro.

Related Articles Quantitative analysis of 1H NMR detected proteins in the rat cerebral cortex in vivo and in vitro.

NMR Biomed. 1993 Jul-Aug;6(4):242-7

Authors: Kauppinen RA, Niskanen T, Hakumäki J, Williams SR

Spectral editing experiments were used to quantify CH3 groups from macromolecular species in the chemical shift region from 1.2 to 1.4 ppm of rat cerebrum in vivo. Two peaks centred at 1.22 and 1.40 ppm were revealed when irradiation was positioned at 4.35 or 4.30 ppm. These peaks had lower saturation factors (1 vs. 1.72 +/- 0.10) than N-acetyl aspartate (NAA) and shorter T2 [60 +/- 5.8 (1.22 ppm) and 51 +/- 2.2 (1.40 ppm) vs. 123 +/- 12 (NAA) ms]. The concentrations of the peaks at 1.22 and 1.40 ppm were calculated to be 0.65 +/- 0.09 and 1.37 +/- 0.18 mmol of CH3 equivalents/kg brain. Acid extract from cerebral cortices contained macromolecular peaks at the same chemical shifts with approximately the same area ratios to NAA as in vivo. These data show that the macromolecular peaks in the brain at TE > 100 ms arise predominantly from proteins which are acid soluble. The assignment of macromolecular signals in the cerebral spectrum to a given polypeptide (thymosin beta 4 and histone H1) is discussed in the light of protein analyses of brain acid extracts.

PMID: 8217525 [PubMed - indexed for MEDLINE]

Source: PubMed

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