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NMR processing:
MDD
NMR assignment:
Backbone:
Autoassign
MARS
UNIO Match
PINE
Side-chains:
UNIO ATNOS-Ascan
NOEs:
UNIO ATNOS-Candid
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:
NOEs, other restraints:
PROSESS
PSVS
RPF scores
iCing
Chemical shifts:
PROSESS
CheShift2
Vasco
iCing
RDCs:
DC
Anisofit
Pseudocontact shifts:
Anisofit
Protein geomtery:
Resolution-by-Proxy
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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Old 11-25-2010, 08:21 PM
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Default Heteronuclear solution-state NMR studies of the chromophore in cyanobacterial phytoch

Heteronuclear solution-state NMR studies of the chromophore in cyanobacterial phytochrome Cph1.

Related Articles Heteronuclear solution-state NMR studies of the chromophore in cyanobacterial phytochrome Cph1.

Biochemistry. 2005 Jun 14;44(23):8244-50

Authors: Strauss HM, Hughes J, Schmieder P

Precise structural information regarding the chromophore binding pocket is essential for an understanding of photochromicity and photoconversion in phytochrome photoreceptors. To this end, we are studying the 59 kDa N-terminal module of the cyanobacterial phytochrome Cph1 from Synechocystis sp. PCC 6803 in both thermally stable forms (Pr and Pfr) using solution-state NMR spectroscopy. The protein is deuterated, while the chromophore, phycocyanobilin (PCB), is isotopically labeled with (15)N or (13)C and (15)N. We have established a simple approach for preparing labeled PCB based on BG11 medium supplemented with an appropriate buffer and NaH(13)CO(3) and Na(15)NO(3) as sole carbon and nitrogen sources, respectively. We show that structural details of the chromophore binding pocket in both Pr and Pfr forms can be obtained using multidimensional heteronuclear solution-state NMR spectroscopy. Using one-dimensional (15)N NMR spectra, we show unequivocally that the chromophore is protonated in both Pr and Pfr states.

PMID: 15938613 [PubMed - indexed for MEDLINE]



Source: PubMed
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