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NMR processing:
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Side-chains:
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NOEs:
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UNIO Candid
ASDP
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Ab initio:
GeNMR
Cyana
XPLOR-NIH
ASDP
UNIO ATNOS-Candid
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Fragment-based:
BMRB CS-Rosetta
Rosetta-NMR (Robetta)
Template-based:
GeNMR
I-TASSER
Refinement:
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Structure from chemical shifts:
Fragment-based:
WeNMR CS-Rosetta
BMRB CS-Rosetta
Homology-based:
CS23D
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Torsion angles from chemical shifts:
Preditor
TALOS
Promega- Proline
Secondary structure from chemical shifts:
CSI (via RCI server)
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MICS caps, β-turns
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Flexibility from chemical shifts:
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Interactions from chemical shifts:
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Chemical shifts re-referencing:
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Methyl S2
B-factor
Molecular dynamics:
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From structure:
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ArShift- Aromatic
ShiftS
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
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Isotope labeling:
UPLABEL
Solid-state NMR:
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Default NMR study on the major mite allergen Der f 2: its refined tertiary structure, epitope

NMR study on the major mite allergen Der f 2: its refined tertiary structure, epitopes for monoclonal antibodies and characteristics shared by ML protein group members.

Related Articles NMR study on the major mite allergen Der f 2: its refined tertiary structure, epitopes for monoclonal antibodies and characteristics shared by ML protein group members.

J Biochem. 2005 Mar;137(3):255-63

Authors: Ichikawa S, Takai T, Inoue T, Yuuki T, Okumura Y, Ogura K, Inagaki F, Hatanaka H

Group 2 major mite allergens Der f 2 and Der p 2 are classified into the recently identified group of MD-2-related lipid-recognition (ML) proteins, but the ligands and biological functions of these allergens are unknown. We have obtained a high-quality NMR structure for Der f 2, and found that it is more similar to the crystal structure of NPC2, a distant homologue, than to that of Der p 2, in terms of the separation and angle between the two major beta-sheets. This made us propose that ML proteins undergo clamshell-like motions that change the sizes of ligand-binding spaces inside their immunoglobulin-fold beta-sandwich to accommodate lipid molecules. This type of motion in lipopolysaccaride recognition of MD-2 is suggested to be likely as well by structural models. We also report the applicability of NMR differential exchange broadening experiments for complexes of intact monoclonal antibodies and antigens; using this technique, we have detected the conformational epitopes for monoclonal antibodies 15E11 and 13A4 as two separate surface patches.

PMID: 15809326 [PubMed - indexed for MEDLINE]



Source: PubMed
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