NMR paper Two-dimensional NMR study of a protein-DNA complex. lac repressor headpiece-operator

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[NMR paper] Two-dimensional NMR study of a protein-DNA complex. lac repressor headpiece-operator

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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, 10:48 PM

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Two-dimensional NMR study of a protein-DNA complex. lac repressor headpiece-operator

Two-dimensional NMR study of a protein-DNA complex. lac repressor headpiece-operator interaction.

Related Articles Two-dimensional NMR study of a protein-DNA complex. lac repressor headpiece-operator interaction.

Biochem Pharmacol. 1990 Jul 1;40(1):89-96

Authors: Kaptein R, Lamerichs RM, Boelens R, Rullmann JA

The interaction of the N-terminal DNA-binding domain (56 amino acid residues) of the lac repressor with lac operator DNA was analyzed using two-dimensional NMR spectroscopy. Both half-operators (11 and 14 bp) and a complete fully symmetric 22 bp operator were studied. Two-dimensional nuclear Overhauser effect (2D NOE) spectra of headpiece-operator complexes were taken in both D2O and H2O solutions. Special attention was given to the problem of 1H resonance assignments. Based on an analysis of the proton-proton NOEs, a model for the headpiece-operator complex could be derived. In this model, most of the protein-DNA contracts occur between amino acid residues in the second helix (recognition helix) of the lac headpiece and DNA bases in the major groove. The orientation of this helix with respect to the dyad axis of the operator is opposite to that found in the X-ray structures of several other repressor-operator complexes.

PMID: 2372315 [PubMed - indexed for MEDLINE]

Source: PubMed

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