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NMR processing:
MDD
NMR assignment:
Backbone:
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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
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Chemical shifts:
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CheShift2
Vasco
iCing
RDCs:
DC
Anisofit
Pseudocontact shifts:
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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 09-13-2020, 09:18 AM
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Default Structural characterization of the N-linked glycans in the receptor binding domain of the SARS-CoV-2 spike protein and*their interactions with human lectins using NMR spectroscopy.

Structural characterization of the N-linked glycans in the receptor binding domain of the SARS-CoV-2 spike protein and*their interactions with human lectins using NMR spectroscopy.

Structural characterization of the N-linked glycans in the receptor binding domain of the SARS-CoV-2 spike protein and*their interactions with human lectins using NMR spectroscopy.

Angew Chem Int Ed Engl. 2020 Sep 11;:

Authors: Lenza MP, Oyenarte I, Diercks T, Quintana JI, Gimeno A, Bosch A, Coelho H, Diniz A, Peccati F, Delgado S, Valle M, Millet O, Abrescia NGA, Palazón A, Marcelo F, Jimenez-Oses G, Jimenez-Barbero J, Arda A, Ereño-Orbea J

Abstract
The glycan structures of the receptor binding domain of the SARS-CoV2 spike glycoprotein expressed in human*HEK293F cells*have been studied by using NMR. The different possible interacting epitopes have been deeply analysed and characterized, providing evidence of the presence of glycan structures*not found*in previous MS-based analyses. The interaction of the RBD*13C-labelled glycans with different*human lectins, which are expressed in different organs and tissues that may be affected during the infection process, has also been evaluated by NMR. In particular,*15N-labelled galectins (galectins-3, -7 and -8 N-terminal), Siglecs (siglec-8, siglec-10), and C-type lectins (DC-SIGN, MGL) have been employed. Complementary experiments*from*the glycoprotein perspective or from the lectin's point of view have permitted to disentangle the specific interacting epitopes in each case. Based on these findings, 3D models of the interacting complexes have been proposed.


PMID: 32915505 [PubMed - as supplied by publisher]



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