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NMR processing:
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NMR assignment:
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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
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Fragment-based:
BMRB CS-Rosetta
Rosetta-NMR (Robetta)
Template-based:
GeNMR
I-TASSER
Refinement:
Amber
Structure from chemical shifts:
Fragment-based:
WeNMR CS-Rosetta
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Homology-based:
CS23D
Simshift
Torsion angles from chemical shifts:
Preditor
TALOS
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Secondary structure from chemical shifts:
CSI (via RCI server)
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MICS caps, β-turns
d2D
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Flexibility from chemical shifts:
RCI
Interactions from chemical shifts:
HADDOCK
Chemical shifts re-referencing:
Shiftcor
UNIO Shiftinspector
LACS
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NMR model quality:
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Vasco
iCing
RDCs:
DC
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Pseudocontact shifts:
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What-If
iCing
PSVS
MolProbity
SAVES2 or SAVES4
Vadar
Prosa
ProQ
MetaMQAPII
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STAN
Ramachandran Plot
Rampage
ERRAT
Verify_3D
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NMR spectrum prediction:
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V-NMR
Flexibility from structure:
Backbone S2
Methyl S2
B-factor
Molecular dynamics:
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Chemical shifts prediction:
From structure:
Shiftx2
Sparta+
Camshift
CH3shift- Methyl
ArShift- Aromatic
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Proshift
PPM
CheShift-2- Cα
From sequence:
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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 Applications of NMR-based PRE and EPR-based DEER spectroscopy to homodimer chain exchange characterization and structure determination.

Applications of NMR-based PRE and EPR-based DEER spectroscopy to homodimer chain exchange characterization and structure determination.

Related Articles Applications of NMR-based PRE and EPR-based DEER spectroscopy to homodimer chain exchange characterization and structure determination.

Methods Mol Biol. 2014;1091:215-27

Authors: Yang Y, Ramelot TA, Ni S, McCarrick RM, Kennedy MA


Abstract
The success of homodimer structure determination by conventional solution NMR spectroscopy relies greatly on interchain distance restraints (less than 6 ┼) derived from nuclear Overhauser effects (NOEs) obtained from (13)C-edited, (12)C-filtered NOESY experiments. However, these experiments may fail when the mixed (13)C-/(12)C-homodimer is never significantly populated due to slow homodimer chain exchange. Thus, knowledge of the homodimer chain exchange kinetics can be put to practical use in preparing samples using the traditional NMR method. Here, we described detailed procedures for using paramagnetic resonance enhancements (PREs) and EPR spectroscopy to measure homodimer chain exchange kinetics. In addition, PRE and EPR methods can be combined to provide mid-range (
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