In vivo protein NMR assignments by PR-NMR

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In vivo protein NMR assignments by PR-NMR

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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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08-03-2005, 07:29 AM

nmrlearner

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Multidimensional NMR Spectroscopy for Protein Characterization and Assignment inside Cells
Patrick N. Reardon and Leonard D. Spicer*
Departments of Biochemistry and Radiology, Duke University Medical Center, Durham, North Carolina 27710
J. Am. Chem. Soc., 127 (31), 10848 -10849, 2005.

Abstract:

High-field, heteronuclear NMR spectroscopy of biological macromolecules in native cellular environments is limited by the low concentrations present and the long data acquisition times needed for the experiments. Successful 1D and 2D heteronuclear NMR data have been reported, but the 3D experiments conventionally used for protein assignment and detailed characterization are generally too long to maintain cell viability. Here we describe the successful in vivo implementation of a suite of fast 3D NMR experiments which we have used to generate the complete backbone assignment of resonances in the recombinant polypeptide GB-1 within Escherichia coli cells. The data were acquired at 600 MHz with a cold probe using the projection reconstruction experiments, (3,2)HNCA, (3,2)HNCO, and (3,2)HA(CA)NH.

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