NMR assignments and the identification of the secondary structure of the anti-retrovi

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NMR assignments and the identification of the secondary structure of the anti-retrovi

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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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11-17-2010, 05:49 PM

nmrlearner

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NMR assignments and the identification of the secondary structure of the anti-retrovi

NMR assignments and the identification of the secondary structure of the anti-retroviral cytidine deaminase.

Related Articles NMR assignments and the identification of the secondary structure of the anti-retroviral cytidine deaminase.

Nucleic Acids Symp Ser (Oxf). 2008;(52):183-4

Authors: Furukawa A, Nagata T, Habu Y, Sugiyama R, Hayashi F, Yokoyama S, Takaku H, Katahira M

APOBEC3G (apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like 3G) is known to have a role in intrinsic cellular immunity against human immunodeficiency virus type1 (HIV-1). The antiretroviral activity of APOBEC3G (APO3G) is associated with the hypermutation of viral DNA through cytidine deamination. APO3G contains two cytidine deaminase domains that are characterised by highly conserved zinc-coordinating motif. It is known that only the C-terminal domain of APO3G (c-APO3G) has the catalytic activity. To shed light on the molecular mechanism of action by which APO3G inactivates HIV-1, we have undertaken the structural and binding studies by NMR. Here, we show the achievement of backbone assignments of c-APO3G and the identification of the secondary structure deduced from chemical shift index (CSI) and NOE data.

PMID: 18776314 [PubMed - indexed for MEDLINE]

Source: PubMed

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