NMR paper Multidimensional NMR spectroscopy of DNA-binding proteins: structure and function of

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[NMR paper] Multidimensional NMR spectroscopy of DNA-binding proteins: structure and function of

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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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08-22-2010, 03:50 AM

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Multidimensional NMR spectroscopy of DNA-binding proteins: structure and function of

Multidimensional NMR spectroscopy of DNA-binding proteins: structure and function of a transcription factor.

Related Articles Multidimensional NMR spectroscopy of DNA-binding proteins: structure and function of a transcription factor.

Toxicol Lett. 1995 Dec;82-83:577-89

Authors: Hsu VL, Jia X, Kearns DR

The solution structure of a type II DNA-binding protein (DBPII), transcription factor 1 (TF1), has been determined using NMR spectroscopy. A multidimensional, heteronuclear strategy was employed to overcome assignment ambiguities due to resonance overlap and broadened crosspeaks. This approach involved the use of selectively deuteriated, 13C- and 15N-labeled samples and 'isotopic heterodimers' to distinguish between intra- and intermonomeric NOEs. A comparison with the crystal structure and NMR analysis of the E. coli HU protein suggests that other homologous proteins in this family will possess similar tertiary structures. This NMR strategy is applicable to the study of other proteins and their biomolecular complexes.

PMID: 8597113 [PubMed - indexed for MEDLINE]

Source: PubMed

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