NMR paper NMR assignments for a helical 40 kDa membrane protein.

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[NMR paper] NMR assignments for a helical 40 kDa membrane protein.

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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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NMR assignments for a helical 40 kDa membrane protein.

NMR assignments for a helical 40 kDa membrane protein.

Related Articles NMR assignments for a helical 40 kDa membrane protein.

J Am Chem Soc. 2004 Apr 28;126(16):5048-9

Authors: Oxenoid K, Kim HJ, Jacob J, Sönnichsen FD, Sanders CR

Backbone nuclear magnetic resonance (NMR) assignments were achieved for diacylglycerol kinase (DAGK) in detergent micelles. DAGK is a homotrimeric integral membrane protein comprised of 121 residue subunits, each having three transmembrane segments. Assignments were made using TROSY-based pulse sequences. DAGK was found to be an almost exclusively helical protein. This work points to the feasibility of both solving the structure of DAGK using solution NMR methods and using NMR as a primary tool in structural studies of other helical integral membrane proteins of similar size and complexity.

PMID: 15099070 [PubMed - indexed for MEDLINE]

Source: PubMed

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