NMR paper Structure and dynamics of the lac repressor-operator complex as determined by NMR.

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[NMR paper] Structure and dynamics of the lac repressor-operator complex as determined by 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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08-22-2010, 03:50 AM

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Structure and dynamics of the lac repressor-operator complex as determined by NMR.

Structure and dynamics of the lac repressor-operator complex as determined by NMR.

Related Articles Structure and dynamics of the lac repressor-operator complex as determined by NMR.

Toxicol Lett. 1995 Dec;82-83:591-9

Authors: Kaptein R, Slijper M, Boelens R

The structures of the lac repressor headpiece and of its complex with an 11 base-pair lac half-operator have been determined by NMR spectroscopy. By 15N relaxation studies the dynamic behavior of the free protein and of the protein in the complex could be established. In the three-helical lac headpiece local backbone mobility was detected in the N-terminal and C-terminal peptide regions and in the loop between helices II and III. Upon DNA binding this loop becomes more rigid and it changes its conformation considerably. The specificity of the protein-DNA interaction follows from a large number of hydrogen-bond and hydrophobic interactions between amino acid side chains and DNA backbone and bases. Restrained molecular dynamics calculations suggest that some of these interactions are dynamic in nature.

PMID: 8597114 [PubMed - indexed for MEDLINE]

Source: PubMed

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