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NMR processing:
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NMR assignment:
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PINE
Side-chains:
UNIO ATNOS-Ascan
NOEs:
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UNIO Candid
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Ab initio:
GeNMR
Cyana
XPLOR-NIH
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Fragment-based:
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Template-based:
GeNMR
I-TASSER
Refinement:
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Structure from chemical shifts:
Fragment-based:
WeNMR CS-Rosetta
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Homology-based:
CS23D
Simshift
Torsion angles from chemical shifts:
Preditor
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Secondary structure from chemical shifts:
CSI (via RCI server)
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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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Chemical shifts:
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RDCs:
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Pseudocontact shifts:
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Protein geomtery:
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PSVS
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SAVES2 or SAVES4
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Verify_3D
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NMR spectrum prediction:
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V-NMR
Flexibility from structure:
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Methyl S2
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Molecular dynamics:
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Chemical shifts prediction:
From structure:
Shiftx2
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CH3shift- Methyl
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Proshift
PPM
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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:
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Default New chemical probes targeting cholesterylation of Sonic Hedgehog in human cells and zebrafish†Electronic supplementary information (ESI) available: Tables S1-S2; Fig. S1-S9, full experimental details and procedures, (1)H/(13)C NMR spectral data of co

New chemical probes targeting cholesterylation of Sonic Hedgehog in human cells and zebrafish†Electronic supplementary information (ESI) available: Tables S1-S2; Fig. S1-S9, full experimental details and procedures, (1)H/(13)C NMR spectral data of compounds 1-6. See DOI: 10.1039/c4sc01600aClick here for additional data file.

Related Articles New chemical probes targeting cholesterylation of Sonic Hedgehog in human cells and zebrafish†Electronic supplementary information (ESI) available: Tables S1-S2; Fig. S1-S9, full experimental details and procedures, (1)H/(13)C NMR spectral data of compounds 1-6. See DOI: 10.1039/c4sc01600aClick here for additional data file.

Chem Sci. 2014 May 1;5(11):4249-4259

Authors: Ciepla P, Konitsiotis AD, Serwa RA, Masumoto N, Leong WP, Dallman MJ, Magee AI, Tate EW

Abstract
Sonic Hedgehog protein (Shh) is a morphogen molecule important in embryonic development and in the progression of many cancer types in which it is aberrantly overexpressed. Fully mature Shh requires attachment of cholesterol and palmitic acid to its C- and N-termini, respectively. The study of lipidated Shh has been challenging due to the limited array of tools available, and the roles of these posttranslational modifications are poorly understood. Herein, we describe the development and validation of optimised alkynyl sterol probes that efficiently tag Shh cholesterylation and enable its visualisation and analysis through bioorthogonal ligation to reporters. An optimised probe was shown to be an excellent cholesterol biomimetic in the context of Shh, enabling appropriate release of tagged Shh from signalling cells, formation of multimeric transport complexes and signalling. We have used this probe to determine the size of transport complexes of lipidated Shh in culture medium and expression levels of endogenous lipidated Shh in pancreatic ductal adenocarcinoma cell lines through quantitative chemical proteomics, as well as direct visualisation of the probe by fluorescence microscopy and detection of cholesterylated Hedgehog protein in developing zebrafish embryos. These sterol probes provide a set of novel and well-validated tools that can be used to investigate the role of lipidation on activity of Shh, and potentially other members of the Hedgehog protein family.


PMID: 25574372 [PubMed - as supplied by publisher]



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