NMR paper Mass spectrometry assisted assignment of NMR resonances in 15N labeled proteins.

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[NMR paper] Mass spectrometry assisted assignment of NMR resonances in 15N labeled proteins.

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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, 10:03 PM

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Mass spectrometry assisted assignment of NMR resonances in 15N labeled proteins.

Mass spectrometry assisted assignment of NMR resonances in 15N labeled proteins.

Related Articles Mass spectrometry assisted assignment of NMR resonances in 15N labeled proteins.

J Am Chem Soc. 2004 Nov 10;126(44):14377-9

Authors: Feng L, Orlando R, Prestegard JH

Application of nuclear magnetic resonance (NMR) methods for the structural characterization to larger and more complex protein systems can be facilitated through the development of new methods for resonance assignment. Here, a novel approach that relies on integration of NMR and mass spectrometry (MS) methods is explored. The approach relies on the fact that both NMR and MS are able to monitor rates of exchange of amide protons for water deuterons. Correlating the rates can connect cross-peak positions from NMR data with fragment masses from MS data to support sequential assignment. The example provided is for a small model protein, ubiquitin, but the potential for application to large, more difficult to express proteins is clear.

PMID: 15521756 [PubMed - indexed for MEDLINE]

Source: PubMed

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