NMR paper NMR dynamics study of the Z-DNA binding domain of human ADAR1 bound to various DNA duplexes.

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[NMR paper] NMR dynamics study of the Z-DNA binding domain of human ADAR1 bound to various DNA duplexes.

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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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03-27-2013, 03:33 PM

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NMR dynamics study of the Z-DNA binding domain of human ADAR1 bound to various DNA duplexes.

Related Articles NMR dynamics study of the Z-DNA binding domain of human ADAR1 bound to various DNA duplexes.

Biochem Biophys Res Commun. 2012 Nov 9;428(1):137-41

Authors: Lee AR, Kim HE, Lee YM, Jeong M, Choi KH, Park JW, Choi YG, Ahn HC, Choi BS, Lee JH

Abstract
The Z-DNA binding domain of human ADAR1 (Z?(ADAR1)) preferentially binds Z-DNA rather than B-DNA with high binding affinity. Here, we have carried out chemical shift perturbation and backbone dynamics studies of Z?(ADAR1) in the free form and in complex with three DNA duplexes, d(CGCGCG)(2), d(CACGTG)(2), and d(CGTACG)(2). This study reveals that Z?(ADAR1) initially binds to d(CGCGCG)(2) through the distinct conformation, especially in the unusually flexible ?1-loop-?2 region, from the d(CGCGCG)(2)-(Z?(ADAR1))(2) complex. This study also suggests that Z?(ADAR1) exhibits a distinct conformational change during the B-Z transition of non-CG-repeat DNA duplexes with low binding affinities compared to the CG-repeat DNA duplex.

PMID: 23079620 [PubMed - indexed for MEDLINE]

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