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PDBsum entry 1qyt

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protein links
Protein binding PDB id
1qyt
Jmol
Contents
Protein chain
11 a.a.
PDB id:
1qyt
Name: Protein binding
Title: Solution structure of fragment (25-35) of beta amyloid peptide in sds micellar solution
Structure: 11-mer peptide from amyloid beta a4 protein. Chain: a. Engineered: yes
Source: Synthetic: yes. Other_details: this sequence occurs naturally in humans.
NMR struc: 21 models
Authors: A.M.D'Ursi,M.R.Armenante,R.Guerrini,S.Salvadori, G.Sorrentino,D.Picone
Key ref: A.M.D'Ursi et al. (2004). Solution structure of amyloid beta-peptide (25-35) in different media. J Med Chem, 47, 4231-4238. PubMed id: 15293994 DOI: 10.1021/jm040773o
Date:
12-Sep-03     Release date:   14-Dec-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

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

 

 
DOI no: 10.1021/jm040773o J Med Chem 47:4231-4238 (2004)
PubMed id: 15293994  
 
 
Solution structure of amyloid beta-peptide (25-35) in different media.
A.M.D'Ursi, M.R.Armenante, R.Guerrini, S.Salvadori, G.Sorrentino, D.Picone.
 
  ABSTRACT  
 
The design of molecules able to interact with the amyloid peptides either as inhibitors of fibril formation or as inhibitors of amyloid membrane pore formation represents one of the most relevant approaches in the development of anti-Alzheimer therapies. Abeta-(25-35), sequence GSNKGAIIGLM, is a highly toxic synthetic derivative of amyloid beta-peptides (Abeta-peptides), which forms fibrillary aggregates. Here, we report the NMR and CD investigation of Abeta-(25-35) in a membrane-mimicking environment and in isotropic mixtures of water and fluoro-alcohols to scan its conformational properties as a function of the medium. The analysis of the 3D structures in the mentioned conditions indicates a propensity of the peptide to behave as a typical transmembrane helix in the lipidic environment. In media characterized by different polarity, it loses the structural regularity at specific points of the sequence as a function of the environment. Furthermore, a comparison with the solution structure of full-length amyloid peptides suggests a role for the 25-27 kink region, which appears to be a general feature of all peptides under the solution conditions explored.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20734314 C.Lee, and S.Ham (2011).
Characterizing amyloid-beta protein misfolding from molecular dynamics simulations with explicit water.
  J Comput Chem, 32, 349-355.  
20336261 G.Wei, A.I.Jewett, and J.E.Shea (2010).
Structural diversity of dimers of the Alzheimer amyloid-beta(25-35) peptide and polymorphism of the resulting fibrils.
  Phys Chem Chem Phys, 12, 3622-3629.  
19093894 B.Bochicchio, M.Lorusso, A.Pepe, and A.M.Tamburro (2009).
On enhancers and inhibitors of elastin-derived amyloidogenesis.
  Nanomed, 4, 31-46.  
19550045 L.Millucci, R.Raggiaschi, D.Franceschini, G.Terstappen, and A.Santucci (2009).
Rapid aggregation and assembly in aqueous solution of A beta (25-35) peptide.
  J Biosci, 34, 293-303.  
19703024 P.Campiglia, M.Scrima, M.Grimaldi, G.Cioffi, A.Bertamino, M.Sala, C.Aquino, I.Gomez-Monterrey, P.Grieco, E.Novellino, and A.M.D'Ursi (2009).
A new series of 1,3-dihidro-imidazo[1,5-c]thiazole-5,7-dione derivatives: synthesis and interaction with Abeta(25-35) amyloid peptide.
  Chem Biol Drug Des, 74, 224-233.  
19025862 A.Taniguchi, M.Skwarczynski, Y.Sohma, T.Okada, K.Ikeda, H.Prakash, H.Mukai, Y.Hayashi, T.Kimura, S.Hirota, K.Matsuzaki, and Y.Kiso (2008).
Controlled production of amyloid beta peptide from a photo-triggered, water-soluble precursor "click peptide".
  Chembiochem, 9, 3055-3065.  
  18453721 K.S.Wun, L.A.Miles, G.A.Crespi, K.Wycherley, D.B.Ascher, K.J.Barnham, R.Cappai, K.Beyreuther, C.L.Masters, M.W.Parker, and W.J.McKinstry (2008).
Crystallization and preliminary X-ray diffraction analysis of the Fab fragment of WO2, an antibody specific for the Abeta peptides associated with Alzheimer's disease.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 64, 438-441.  
18515070 L.M.Gordon, A.Nisthal, A.B.Lee, S.Eskandari, P.Ruchala, C.L.Jung, A.J.Waring, and P.W.Mobley (2008).
Structural and functional properties of peptides based on the N-terminus of HIV-1 gp41 and the C-terminus of the amyloid-beta protein.
  Biochim Biophys Acta, 1778, 2127-2137.  
18228239 M.Valerio, F.Porcelli, J.P.Zbilut, A.Giuliani, C.Manetti, and F.Conti (2008).
pH effects on the conformational preferences of amyloid beta-peptide (1-40) in HFIP aqueous solution by NMR spectroscopy.
  ChemMedChem, 3, 833-843.  
18512763 Z.K.Sun, H.Q.Yang, J.Pan, H.Zhen, Z.Q.Wang, S.D.Chen, and J.Q.Ding (2008).
Protective effects of erythropoietin on tau phosphorylation induced by beta-amyloid.
  J Neurosci Res, 86, 3018-3027.  
17152078 L.Ronga, E.Langella, P.Palladino, D.Marasco, B.Tizzano, M.Saviano, C.Pedone, R.Improta, and M.Ruvo (2007).
Does tetracycline bind helix 2 of prion? An integrated spectroscopical and computational study of the interaction between the antibiotic and alpha helix 2 human prion protein fragments.
  Proteins, 66, 707-715.  
17381724 P.Campiglia, C.Esposito, M.Scrima, I.Gomez-Monterrey, A.Bertamino, P.Grieco, E.Novellino, and A.M.D'Ursi (2007).
Conformational stability of Abeta-(25-35) in the presence of thiazolidine derivatives.
  Chem Biol Drug Des, 69, 111-118.  
17091525 S.Jaroch (2007).
A Soluble Amyloid Fibril Segment to Study Aggregate Formation.
  ChemMedChem, 2, 47-49.  
17534931 S.Rodziewicz-Motowidło, P.Juszczyk, A.S.Kołodziejczyk, E.Sikorska, A.Skwierawska, M.Oleszczuk, and Z.Grzonka (2007).
Conformational solution studies of the SDS micelle-bound 11-28 fragment of two Alzheimer's beta-amyloid variants (E22K and A21G) using CD, NMR, and MD techniques.
  Biopolymers, 87, 23-39.  
16500972 B.Ma, and R.Nussinov (2006).
The stability of monomeric intermediates controls amyloid formation: Abeta25-35 and its N27Q mutant.
  Biophys J, 90, 3365-3374.  
17131288 C.Esposito, A.Tedeschi, M.Scrima, G.D'errico, M.F.Ottaviani, P.Rovero, and A.M.D'ursi (2006).
Exploring interaction of beta-amyloid segment (25-35) with membrane models through paramagnetic probes.
  J Pept Sci, 12, 766-774.  
16766615 G.Wei, and J.E.Shea (2006).
Effects of solvent on the structure of the Alzheimer amyloid-beta(25-35) peptide.
  Biophys J, 91, 1638-1647.  
16444756 S.Tomaselli, V.Esposito, P.Vangone, N.A.van Nuland, A.M.Bonvin, R.Guerrini, T.Tancredi, P.A.Temussi, and D.Picone (2006).
The alpha-to-beta conformational transition of Alzheimer's Abeta-(1-42) peptide in aqueous media is reversible: a step by step conformational analysis suggests the location of beta conformation seeding.
  Chembiochem, 7, 257-267.
PDB code: 1z0q
16823798 Y.L.Lyubchenko, S.Sherman, L.S.Shlyakhtenko, and V.N.Uversky (2006).
Nanoimaging for protein misfolding and related diseases.
  J Cell Biochem, 99, 52-70.  
15761877 Y.Sohma, Y.Hayashi, M.Kimura, Y.Chiyomori, A.Taniguchi, M.Sasaki, T.Kimura, and Y.Kiso (2005).
The 'O-acyl isopeptide method' for the synthesis of difficult sequence-containing peptides: application to the synthesis of Alzheimer's disease-related amyloid beta peptide (Abeta) 1-42.
  J Pept Sci, 11, 441-451.  
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. Where a reference describes a PDB structure, the PDB code is shown on the right.