NMR paper An NMR method for studying the kinetics of metal exchange in biomolecular systems.

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[NMR paper] An NMR method for studying the kinetics of metal exchange in biomolecular systems.

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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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11-24-2010, 08:58 PM

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An NMR method for studying the kinetics of metal exchange in biomolecular systems.

An NMR method for studying the kinetics of metal exchange in biomolecular systems.

Related Articles An NMR method for studying the kinetics of metal exchange in biomolecular systems.

J Biomol NMR. 2002 Aug;23(4):303-9

Authors: Barbieri R, Hore PJ, Luchina C, Pierattelli R

The kinetics of lanthanide (III) exchange for calcium(II) in the C-terminal EF-hand of the protein calbindin D9k have been studied by one-dimensional (1D) stopped-flow NMR. By choosing a paramagnetic lanthanide (Ce3+), kinetics in the sub-second range can be easily measured. This is made possible by the fact that (i) the kinetic behaviour of hyperfine shifted signals can be monitored in ID NMR and (ii) fast repetition rates can be employed because these hyperfine shifted signals relax fast. It is found that the Ce3+-Ca2+ exchange process indeed takes place on a sub-second timescale and can be easily monitored with this technique. As the rate of calcium-cerium substitution was found not to depend on the presence of excess calcium in solution, the kinetics of the process were interpreted in terms of a bimolecular associative mechanism, and the rate constants extracted. Interestingly, the dissociative mechanism involving the apo form of the protein, which is generally assumed for metal ion exchange at protein binding sites, was not in agreement with our data.

PMID: 12398350 [PubMed - indexed for MEDLINE]

Source: PubMed

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