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NMR processing:
MDD
NMR assignment:
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MARS
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PINE
Side-chains:
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NOEs:
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UNIO Candid
ASDP
Structure from NMR restraints:
Ab initio:
GeNMR
Cyana
XPLOR-NIH
ASDP
UNIO ATNOS-Candid
UNIO Candid
Fragment-based:
BMRB CS-Rosetta
Rosetta-NMR (Robetta)
Template-based:
GeNMR
I-TASSER
Refinement:
Amber
Structure from chemical shifts:
Fragment-based:
WeNMR CS-Rosetta
BMRB CS-Rosetta
Homology-based:
CS23D
Simshift
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:
Shiftcor
UNIO Shiftinspector
LACS
CheckShift
RefDB
NMR model quality:
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RPF scores
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Chemical shifts:
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Vasco
iCing
RDCs:
DC
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Pseudocontact shifts:
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PROSESS
What-If
iCing
PSVS
MolProbity
SAVES2 or SAVES4
Vadar
Prosa
ProQ
MetaMQAPII
PSQS
Eval123D
STAN
Ramachandran Plot
Rampage
ERRAT
Verify_3D
Harmony
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:
camLILA
ccSOL
Camfold
camGroEL
Zyggregator
Isotope labeling:
UPLABEL
Solid-state NMR:
sedNMR


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Default The zinc-binding fragment of HypA from Helicobacter pylori: a tempting site also for nickel ions.

The zinc-binding fragment of HypA from Helicobacter pylori: a tempting site also for nickel ions.

Related Articles The zinc-binding fragment of HypA from Helicobacter pylori: a tempting site also for nickel ions.

Dalton Trans. 2013 Jan 21;

Authors: Rowinska-Zyrek M, Potocki S, Witkowska D, Valensin D, Kozlowski H

Abstract
HypA, a nickel accessory protein from H. pylori, binds a zinc ion in it's structural site, a loop with two conserved CXXC motifs (Ac-ELECKDCSHVFKPNALDYGVCEKCHS-NH(2)). There are at least three hypotheses on the binding mode of this ion. In this paper, we try to understand how Zn(2+) binds to this fragment and why Ni(2+), a metal with quite a high affinity towards thiolic sites, doesn't compete with zinc in the binding to this motif. Potentiometric titrations, mass spectrometry, NMR, UV-Vis and CD spectroscopy help us to compare the coordination modes in both metal complexes and discuss their thermodynamic stabilities.


PMID: 23338727 [PubMed - as supplied by publisher]



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