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PDBsum entry 1ba4

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protein links
Glycoprotein PDB id
1ba4
Jmol
Contents
Protein chain
40 a.a. *
* Residue conservation analysis
PDB id:
1ba4
Name: Glycoprotein
Title: The solution structure of amyloid beta-peptide (1-40) in a water-micelle environment. Is the membrane-spanning domain where we think it is? nmr, 10 structures
Structure: Amyloid beta-peptide. Chain: a. Fragment: abeta. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: unidentified. Expression_system_taxid: 32644
NMR struc: 10 models
Authors: M.Coles,W.Bicknell,A.A.Watson,D.P.Fairlie,D.J.Craik
Key ref:
M.Coles et al. (1998). Solution structure of amyloid beta-peptide(1-40) in a water-micelle environment. Is the membrane-spanning domain where we think it is? Biochemistry, 37, 11064-11077. PubMed id: 9693002 DOI: 10.1021/bi972979f
Date:
07-Apr-98     Release date:   17-Jun-98    
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.
40 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     integral to membrane   1 term 
  Biological process     nervous system development   1 term 

 

 
DOI no: 10.1021/bi972979f Biochemistry 37:11064-11077 (1998)
PubMed id: 9693002  
 
 
Solution structure of amyloid beta-peptide(1-40) in a water-micelle environment. Is the membrane-spanning domain where we think it is?
M.Coles, W.Bicknell, A.A.Watson, D.P.Fairlie, D.J.Craik.
 
  ABSTRACT  
 
The three-dimensional solution structure of the 40 residue amyloid beta-peptide, Abeta(1-40), has been determined using NMR spectroscopy at pH 5.1, in aqueous sodium dodecyl sulfate (SDS) micelles. In this environment, which simulates to some extent a water-membrane medium, the peptide is unstructured between residues 1 and 14 which are mainly polar and likely solvated by water. However, the rest of the protein adopts an alpha-helical conformation between residues 15 and 36 with a kink or hinge at 25-27. This largely hydrophobic region is likely solvated by SDS. Based on the derived structures, evidence is provided in support of a possible new location for the transmembrane domain of Abeta within the amyloid precursor protein (APP). Studies between pH 4.2 and 7.9 reveal a pH-dependent helix-coil conformational switch. At the lower pH values, where the carboxylate residues are protonated, the helix is uncharged, intact, and lipid-soluble. As the pH increases above 6. 0, part of the helical region (15-24) becomes less structured, particularly near residues E22 and D23 where deprotonation appears to facilitate unwinding of the helix. This pH-dependent unfolding to a random coil conformation precedes any tendency of this peptide to aggregate to a beta-sheet as the pH increases. The structural biology described herein for Abeta(1-40) suggests that (i) the C-terminal two-thirds of the peptide is an alpha-helix in membrane-like environments, (ii) deprotonation of two acidic amino acids in the helix promotes a helix-coil conformational transition that precedes aggregation, (iii) a mobile hinge exists in the helical region of Abeta(1-40) and this may be relevant to its membrane-inserting properties and conformational rearrangements, and (iv) the location of the transmembrane domain of amyloid precursor proteins may be different from that accepted in the literature. These results may provide new insight to the structural properties of amyloid beta-peptides of relevance to Alzheimer's disease.
 

Literature references that cite this PDB file's key reference

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NMR structure in a membrane environment reveals putative amyloidogenic regions of the SEVI precursor peptide PAP(248-286).
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PDB code: 2l3h
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Dynamic {alpha}-Helix Structure of Micelle-bound Human Amylin.
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PDB code: 2kb8
18702528 A.J.Beel, C.K.Mobley, H.J.Kim, F.Tian, A.Hadziselimovic, B.Jap, J.H.Prestegard, and C.R.Sanders (2008).
Structural studies of the transmembrane C-terminal domain of the amyloid precursor protein (APP): does APP function as a cholesterol sensor?
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18305836 A.Rauk (2008).
Why is the amyloid beta peptide of Alzheimer's disease neurotoxic?
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18479708 B.Tarus, J.E.Straub, and D.Thirumalai (2008).
Structures and free-energy landscapes of the wild type and mutants of the Abeta(21-30) peptide are determined by an interplay between intrapeptide electrostatic and hydrophobic interactions.
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18390616 D.H.Kim, and J.A.Frangos (2008).
Effects of amyloid beta-peptides on the lysis tension of lipid bilayer vesicles containing oxysterols.
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Molecular modeling of zinc and copper binding with Alzheimer's amyloid beta-peptide.
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18219465 J.D.Gehman, C.C.O'Brien, F.Shabanpoor, J.D.Wade, and F.Separovic (2008).
Metal effects on the membrane interactions of amyloid-beta peptides.
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Structure of amyloid beta fragments in aqueous environments.
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PDB code: 1x1p
16731975 M.Bisaglia, A.Trolio, M.Bellanda, E.Bergantino, L.Bubacco, and S.Mammi (2006).
Structure and topology of the non-amyloid-beta component fragment of human alpha-synuclein bound to micelles: implications for the aggregation process.
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16618124 P.C.Keller, T.Tomita, I.Hayashi, D.Chandu, J.D.Weber, D.P.Cistola, and R.Kopan (2006).
A faster migrating variant masquerades as NICD when performing in vitro gamma-secretase assays with bacterially expressed Notch substrates.
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16807784 P.K.Mandal, J.W.Pettegrew, D.W.McKeag, and R.Mandal (2006).
Alzheimer's disease: halothane induces Abeta peptide to oligomeric form--solution NMR studies.
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16301322 S.Zirah, S.A.Kozin, A.K.Mazur, A.Blond, M.Cheminant, I.Ségalas-Milazzo, P.Debey, and S.Rebuffat (2006).
Structural changes of region 1-16 of the Alzheimer disease amyloid beta-peptide upon zinc binding and in vitro aging.
  J Biol Chem, 281, 2151-2161.
PDB codes: 1ze7 1ze9 2bp4
17051221 Y.Shen, A.Joachimiak, M.R.Rosner, and W.J.Tang (2006).
Structures of human insulin-degrading enzyme reveal a new substrate recognition mechanism.
  Nature, 443, 870-874.
PDB codes: 2g47 2g48 2g49 2g54 2g56
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Controlling {beta}-amyloid oligomerization by the use of naphthalene sulfonates: trapping low molecular weight oligomeric species.
  J Biol Chem, 280, 34747-34754.  
15889393 C.E.Giacomelli, and W.Norde (2005).
Conformational changes of the amyloid beta-peptide (1-40) adsorbed on solid surfaces.
  Macromol Biosci, 5, 401-407.  
15557279 D.V.Laurents, P.M.Gorman, M.Guo, M.Rico, A.Chakrabartty, and M.Bruix (2005).
Alzheimer's Abeta40 studied by NMR at low pH reveals that sodium 4,4-dimethyl-4-silapentane-1-sulfonate (DSS) binds and promotes beta-ball oligomerization.
  J Biol Chem, 280, 3675-3685.  
  15639796 G.C.Gregory, and G.M.Halliday (2005).
What is the dominant Abeta species in human brain tissue? A review.
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16339896 L.Cruz, B.Urbanc, J.M.Borreguero, N.D.Lazo, D.B.Teplow, and H.E.Stanley (2005).
Solvent and mutation effects on the nucleation of amyloid beta-protein folding.
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15526299 M.Valerio, A.Colosimo, F.Conti, A.Giuliani, A.Grottesi, C.Manetti, and J.P.Zbilut (2005).
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15930005 N.D.Lazo, M.A.Grant, M.C.Condron, A.C.Rigby, and D.B.Teplow (2005).
On the nucleation of amyloid beta-protein monomer folding.
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Conformational transition of amyloid beta-peptide.
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15454432 B.Urbanc, L.Cruz, F.Ding, D.Sammond, S.Khare, S.V.Buldyrev, H.E.Stanley, and N.V.Dokholyan (2004).
Molecular dynamics simulation of amyloid beta dimer formation.
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15583128 B.Urbanc, L.Cruz, S.Yun, S.V.Buldyrev, G.Bitan, D.B.Teplow, and H.E.Stanley (2004).
In silico study of amyloid beta-protein folding and oligomerization.
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15345552 C.Ege, and K.Y.Lee (2004).
Insertion of Alzheimer's A beta 40 peptide into lipid monolayers.
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15649580 C.Morgan, M.Colombres, M.T.Nuñez, and N.C.Inestrosa (2004).
Structure and function of amyloid in Alzheimer's disease.
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15172731 D.A.Butterfield, and A.I.Bush (2004).
Alzheimer's amyloid beta-peptide (1-42): involvement of methionine residue 35 in the oxidative stress and neurotoxicity properties of this peptide.
  Neurobiol Aging, 25, 563-568.  
15189856 D.L.Mobley, D.L.Cox, R.R.Singh, M.W.Maddox, and M.L.Longo (2004).
Modeling amyloid beta-peptide insertion into lipid bilayers.
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15298911 S.Micelli, D.Meleleo, V.Picciarelli, M.G.Stoico, and E.Gallucci (2004).
Effect of nanomolar concentrations of sodium dodecyl sulfate, a catalytic inductor of alpha-helices, on human calcitonin incorporation and channel formation in planar lipid membranes.
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Discrete molecular dynamics simulations of peptide aggregation.
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The transmembrane domain of the amyloid precursor protein in microsomal membranes is on both sides shorter than predicted.
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Metal ions, pH, and cholesterol regulate the interactions of Alzheimer's disease amyloid-beta peptide with membrane lipid.
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Protein aggregation/folding: the role of deterministic singularities of sequence hydrophobicity as determined by nonlinear signal analysis of acylphosphatase and Abeta(1-40).
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Substitution of isoleucine-31 by helical-breaking proline abolishes oxidative stress and neurotoxic properties of Alzheimer's amyloid beta-peptide.
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Oxidation of methionine 35 attenuates formation of amyloid beta -peptide 1-40 oligomers.
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Solution structure of the Alzheimer amyloid beta-peptide (1-42) in an apolar microenvironment. Similarity with a virus fusion domain.
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PDB code: 1iyt
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The intramembrane cleavage site of the amyloid precursor protein depends on the length of its transmembrane domain.
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11741923 S.R.Ji, Y.Wu, and S.F.Sui (2002).
Cholesterol is an important factor affecting the membrane insertion of beta-amyloid peptide (A beta 1-40), which may potentially inhibit the fibril formation.
  J Biol Chem, 277, 6273-6279.  
12149256 Y.Fezoui, and D.B.Teplow (2002).
Kinetic studies of amyloid beta-protein fibril assembly. Differential effects of alpha-helix stabilization.
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11606220 K.Watanabe, T.Segawa, K.Nakamura, M.Kodaka, T.Konakahara, and H.Okuno (2001).
Identification of the molecular interaction site of amyloid beta peptide by using a fluorescence assay.
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Oxidative and hydrolytic properties of beta-amyloid.
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NMR studies in aqueous solution fail to identify significant conformational differences between the monomeric forms of two Alzheimer peptides with widely different plaque-competence, A beta(1-40)(ox) and A beta(1-42)(ox).
  Eur J Biochem, 268, 5930-5936.  
10936205 C.S.Atwood, R.C.Scarpa, X.Huang, R.D.Moir, W.D.Jones, D.P.Fairlie, R.E.Tanzi, and A.I.Bush (2000).
Characterization of copper interactions with alzheimer amyloid beta peptides: identification of an attomolar-affinity copper binding site on amyloid beta1-42.
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Alzheimer's amyloid fibrils: structure and assembly.
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Structure of a biologically active fragment of human serum apolipoprotein C-II in the presence of sodium dodecyl sulfate and dodecylphosphocholine.
  Biochim Biophys Acta, 1486, 253-264.
PDB code: 1by6
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Mutational analysis of designed peptides that undergo structural transition from alpha helix to beta sheet and amyloid fibril formation.
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An atomic model for the pleated beta-sheet structure of Abeta amyloid protofilaments.
  Biophys J, 76, 2871-2878.  
10428074 L.Lins, A.Thomas-Soumarmon, T.Pillot, J.Vandekerchkhove, M.Rosseneu, and R.Brasseur (1999).
Molecular determinants of the interaction between the C-terminal domain of Alzheimer's beta-amyloid peptide and apolipoprotein E alpha-helices.
  J Neurochem, 73, 758-769.  
10516572 M.Pellegrini, and D.F.Mierke (1999).
Structural characterization of peptide hormone/receptor interactions by NMR spectroscopy.
  Biopolymers, 51, 208-220.  
9737846 A.A.Watson, D.P.Fairlie, and D.J.Craik (1998).
Solution structure of methionine-oxidized amyloid beta-peptide (1-40). Does oxidation affect conformational switching?
  Biochemistry, 37, 12700-12706.
PDB code: 1ba6
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.