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PDBsum entry 2bom

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protein Protein-protein interface(s) links
Serine protease inhibitor PDB id
2bom
Jmol
Contents
Protein chains
33 a.a.
Theoretical model
PDB id:
2bom
Name: Serine protease inhibitor
Title: Model of alzheimer's disease amyloid-beta peptide based on a RNA binding protein
Structure: Amyloid beta a4. Synonym: amyloid beta. Chain: a, b
Source: Homo sapiens
Authors: V.S.Mathura,D.Paris,G.Ait-Ghezala,A.Quadros,N.S.Patel, D.N.Kolippakkam,C.H.Volmar,M.J.Mullan
Key ref: V.S.Mathura et al. (2005). Model of Alzheimer's disease amyloid-beta peptide based on a RNA binding protein. Biochem Biophys Res Commun, 332, 585-592. PubMed id: 15896718 DOI: 10.1016/j.bbrc.2005.04.164
Date:
12-Apr-05     Release date:   14-Apr-05    
PROCHECK
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 Headers
 References

Protein chains
Pfam   ArchSchema ?
P05067  (A4_HUMAN) -  Amyloid beta A4 protein
Seq:
Struc:
 
Seq:
Struc:
770 a.a.
33 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure

 

 
DOI no: 10.1016/j.bbrc.2005.04.164 Biochem Biophys Res Commun 332:585-592 (2005)
PubMed id: 15896718  
 
 
Model of Alzheimer's disease amyloid-beta peptide based on a RNA binding protein.
V.S.Mathura, D.Paris, G.Ait-Ghezala, A.Quadros, N.S.Patel, D.N.Kolippakkam, C.H.Volmar, M.J.Mullan.
 
  ABSTRACT  
 
Although Alzheimer's Abeta peptide has been shown to form beta-sheet structure, a high-resolution molecular structure is still unavailable to date. A search for a sequence neighbor using Abeta(10-42) as the query in the Protein Data-Bank (PDB) revealed that an RNA binding protein, AF-Sm1 from Archaeoglobus fulgidus (PDB entry: 1i4k chain Z), shared 36% identical residues. Using AF-Sm1 as a template, we built a molecular model of Abeta(10-42) by applying comparative modeling methods. The model of Abeta(10-42) contains an antiparallel beta-sheet formed by residues 16-23 and 32-41. Hydrophobic surface constituted by residues 17-20 (LVFF) separates distinctly charged regions. Residues that interact with RNA in the AF-Sm1 crystal structure were found to be conserved in Abeta. Using a native gel we demonstrate for the first time that RNA can interact with Abeta and selectively retard the formation of fibrils or higher-order oligomers. We hypothesize that in a similar fashion to AF-Sm1, RNA interacts with Abeta in the beta-hairpin (beta-turn-beta) structure and prevents fibril formation.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
19818105 N.S.Patel, V.S.Mathura, C.Bachmeier, D.Beaulieu-Abdelahad, V.Laporte, O.Weeks, M.Mullan, and D.Paris (2010).
Alzheimer's beta-amyloid peptide blocks vascular endothelial growth factor mediated signaling via direct interaction with VEGFR-2.
  J Neurochem, 112, 66-76.  
18266117 N.S.Patel, A.Quadros, S.Brem, M.Wotoczek-Obadia, V.S.Mathura, V.Laporte, M.Mullan, and D.Paris (2008).
Potent anti-angiogenic motifs within the Alzheimer beta-amyloid peptide.
  Amyloid, 15, 5.  
17211889 F.Dulin, I.Callebaut, N.Colloc'h, and J.P.Mornon (2007).
Sequence-based modeling of Abeta42 soluble oligomers.
  Biopolymers, 85, 422-437.  
16880933 H.Koga (2006).
Establishment of the platform for reverse chemical genetics targeting novel protein-protein interactions.
  Mol Biosyst, 2, 159-164.  
16650066 S.Parry, D.Todorova-Balvay, T.Srikrishnan, and E.Sulkowski (2005).
Thiophilic interaction chromatography of Alzheimer's beta-amyloid peptides.
  J Pept Res, 66, 99.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time.