NMR paper Investigation of oxidation state-dependent conformational changes in Desulfovibrio vu

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[NMR paper] Investigation of oxidation state-dependent conformational changes in Desulfovibrio vu

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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, 02:27 PM

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Investigation of oxidation state-dependent conformational changes in Desulfovibrio vu

Investigation of oxidation state-dependent conformational changes in Desulfovibrio vulgaris Hildenborough cytochrome c553 by two-dimensional H-NMR spectra.

Related Articles Investigation of oxidation state-dependent conformational changes in Desulfovibrio vulgaris Hildenborough cytochrome c553 by two-dimensional H-NMR spectra.

FEBS Lett. 1996 Jul 1;389(2):203-9

Authors: Blanchard L, Blackledge MJ, Marion D, Guerlesquin F

Two-dimensional nuclear magnetic resonance spectroscopy (2D-NMR) was used to assign the proton resonances of ferricytochrome C553 from Desulfovibrio vulgaris Hildenborough. The spin systems of 76 out of 79 amino acids were identified by J-correlation spectroscopy (COSY and HOHAHA) in H20 and D20 and correlated by nuclear Overhauser effect spectroscopy (NOESY). The proton chemical shifts are compared in both oxidized and reduced states of the protein at 23 degrees C and pH 5.9. Chemical shift variations between reduced and oxidized states are due to the paramagnetic contribution. Medium and long-range nOe demonstrate the lack of major changes between the two redox states. NMR data provide evidence that in this low oxidoreduction potential cytochrome, the oxidized state is more rigid than the reduced state.

PMID: 8766830 [PubMed - indexed for MEDLINE]

Source: PubMed

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