spacer
spacer

PDBsum entry 2beg

Go to PDB code: 
protein Protein-protein interface(s) links
Protein fibril PDB id
2beg
Jmol
Contents
Protein chains
26 a.a. *
* Residue conservation analysis
PDB id:
2beg
Name: Protein fibril
Title: 3d structure of alzheimer's abeta(1-42) fibrils
Structure: Amyloid beta a4 protein. Chain: a, b, c, d, e. Fragment: beta-amyloid protein 42. Synonym: app, abpp, alzheimer's disease amyloid protein, cerebral vascular amyloid peptide, cvap, protease nexin-ii, pn-ii, appi. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: app. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
NMR struc: 10 models
Authors: T.Luhrs,C.Ritter,M.Adrian,D.Riek-Loher,B.Bohrmann,H.Dobeli, D.Schubert,R.Riek
Key ref:
T.Lührs et al. (2005). 3D structure of Alzheimer's amyloid-beta(1-42) fibrils. Proc Natl Acad Sci U S A, 102, 17342-17347. PubMed id: 16293696 DOI: 10.1073/pnas.0506723102
Date:
24-Oct-05     Release date:   22-Nov-05    
PROCHECK
Go to PROCHECK summary
 Headers
 References

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

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

 

 
DOI no: 10.1073/pnas.0506723102 Proc Natl Acad Sci U S A 102:17342-17347 (2005)
PubMed id: 16293696  
 
 
3D structure of Alzheimer's amyloid-beta(1-42) fibrils.
T.Lührs, C.Ritter, M.Adrian, D.Riek-Loher, B.Bohrmann, H.Döbeli, D.Schubert, R.Riek.
 
  ABSTRACT  
 
Alzheimer's disease is the most fatal neurodegenerative disorder wherein the process of amyloid-beta (Abeta) amyloidogenesis appears causative. Here, we present the 3D structure of the fibrils comprising Abeta(1-42), which was obtained by using hydrogen-bonding constraints from quenched hydrogen/deuterium-exchange NMR, side-chain packing constraints from pairwise mutagenesis studies, and parallel, in-register beta-sheet arrangement from previous solid-state NMR studies. Although residues 1-17 are disordered, residues 18-42 form a beta-strand-turn-beta-strand motif that contains two intermolecular, parallel, in-register beta-sheets that are formed by residues 18-26 (beta1) and 31-42 (beta2). At least two molecules of Abeta(1-42) are required to achieve the repeating structure of a protofilament. Intermolecular side-chain contacts are formed between the odd-numbered residues of strand beta1 of the nth molecule and the even-numbered residues of strand beta2 of the (n - 1)th molecule. This interaction pattern leads to partially unpaired beta-strands at the fibrillar ends, which explains the sequence selectivity, the cooperativity, and the apparent unidirectionality of Abeta fibril growth. It also provides a structural basis for fibrillization inhibitors.
 
  Selected figure(s)  
 
Figure 2.
Fig. 2. Pairwise mutagenesis of 35LA (1-42) peptides. (A) Cartoon of intramolecular versus domain swapping-type interaction between monomers in the A (1-42) protofilament that consists of parallel, in-register -sheets exemplified by the salt bridge formed between the charged residues D23 and K28. Individual A molecules are indicated as colored bars that correspond to a cross section along the protofilament axis through the C^ atom positions of one presumed interacting pair of amino acids. The identity of each variant A peptide is indicated next to the corresponding schemes in rows 1-4. "intra" denotes the intramolecular scenario, and "inter" indicates the domain swapping-type scenario. Red diagonal crosses mark all scenarios that were considered to be incompatible with WT fibril formation. (B-J) Negative staining electron microscopy of 35LA (1-42) peptides. The variants are indicated on each image. All electron micrographs were recorded at a nominal magnification of x72,000. (Scale bar, 100 nm.
Figure 4.
Fig. 4. The 3D structure of a 35MoxA (1-42) fibril. (A and B) Ribbon diagrams of the core structure of residues 17-42 illustrating the intermolecular nature of the inter- -strand interactions. Individual molecules are colored. For example, the monomer at the odd end is shown in cyan. The -strands are indicated by arrows, nonregular secondary structure is indicated by spline curves through the C^ atom coordinates of the corresponding residues, and the bonds of side chains that constitute the core of the protofilament are shown. In B, the intermolecular salt bridge between residues D23 and K28 is indicated by dotted lines, and the two salt bridges formed by the central A (1-42) molecule are highlighted by rectangles. (C) van der Waals contact surface polarity and ribbon diagram at the odd end of the 35MoxA (1-42) protofilament comprising residues 17-42. The -sheets are indicated by cyan arrows, and nonregular secondary structure is indicated by gray spline curves. The hydrophobic, polar, negatively charged, and positively charged amino acid side chains are shown in yellow, green, red, and blue, respectively. Positively and negatively charged surface patches are shown in blue and red, respectively, and all others are shown in white. The direction of the fibril axis is indicated by an arrow pointing from even to odd. (D)(Upper) Simulation of a 35MoxA (1-42) fibril that consists of four protofilaments colored individually. Lower shows the same fibril in a noisy gray-scale image, which has been blurred corresponding to a resolution of 2 nm. In Right,a x5-magnified cross section perpendicular to the fibril axis is shown, using the same color code. Dimensions are indicated. To match the experimental twist of the protofilament of the fibril shown in E, a twist angle of 0.45° per molecule was used. (E) Two examples of cryoelectron micrographs of single 35MoxA (1-42) fibrils. (Scale bar, 50 nm.
 
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
  21457473 A.A.Reinke, and J.E.Gestwicki (2011).
Insight into amyloid structure using chemical probes.
  Chem Biol Drug Des, 77, 399-411.  
20926137 A.Budimir, N.Humbert, M.Elhabiri, I.Osinska, M.Biruš, and A.M.Albrecht-Gary (2011).
Hydroxyquinoline based binders: promising ligands for chelatotherapy?
  J Inorg Biochem, 105, 490-496.  
21406339 A.Budimir (2011).
Metal ions, Alzheimer's disease and chelation therapy.
  Acta Pharm, 61, 1.  
21325059 B.Winner, R.Jappelli, S.K.Maji, P.A.Desplats, L.Boyer, S.Aigner, C.Hetzer, T.Loher, M.Vilar, S.Campioni, C.Tzitzilonis, A.Soragni, S.Jessberger, H.Mira, A.Consiglio, E.Pham, E.Masliah, F.H.Gage, and R.Riek (2011).
In vivo demonstration that {alpha}-synuclein oligomers are toxic.
  Proc Natl Acad Sci U S A, 108, 4194-4199.  
  21258392 C.Bleiholder, N.F.Dupuis, T.Wyttenbach, and M.T.Bowers (2011).
Ion mobility-mass spectrometry reveals a conformational conversion from random assembly to β-sheet in amyloid fibril formation.
  Nat Chem, 3, 172-177.  
21376731 C.Haupt, M.Bereza, S.T.Kumar, B.Kieninger, I.Morgado, P.Hortschansky, G.Fritz, C.Röcken, U.Horn, and M.Fändrich (2011).
Pattern recognition with a fibril-specific antibody fragment reveals the surface variability of natural amyloid fibrils.
  J Mol Biol, 408, 529-540.  
20941707 C.L.Heldt, S.Zhang, and G.Belfort (2011).
Asymmetric amyloid fibril elongation: a new perspective on a symmetric world.
  Proteins, 79, 92-98.  
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.  
21371882 C.Wu, and J.E.Shea (2011).
Coarse-grained models for protein aggregation.
  Curr Opin Struct Biol, 21, 209-220.  
21319744 J.Zheng, C.Liu, M.R.Sawaya, B.Vadla, S.Khan, R.J.Woods, D.Eisenberg, W.J.Goux, and J.S.Nowick (2011).
Macrocyclic β-Sheet Peptides That Inhibit the Aggregation of a Tau-Protein-Derived Hexapeptide.
  J Am Chem Soc, 133, 3144-3157.  
20954203 K.Numata, and D.L.Kaplan (2011).
Differences in cytotoxicity of β-sheet peptides originated from silk and amyloid β.
  Macromol Biosci, 11, 60-64.  
21290543 M.Dasari, A.Espargaro, R.Sabate, J.M.Lopez Del Amo, U.Fink, G.Grelle, J.Bieschke, S.Ventura, and B.Reif (2011).
Bacterial Inclusion Bodies of Alzheimer's Disease β-Amyloid Peptides Can Be Employed To Study Native-Like Aggregation Intermediate States.
  Chembiochem, 12, 407-423.  
21408230 M.Ito, J.Johansson, R.Strömberg, and L.Nilsson (2011).
Unfolding of the amyloid β-peptide central helix: mechanistic insights from molecular dynamics simulations.
  PLoS One, 6, e17587.  
22037310 N.L.Fawzi, J.Ying, R.Ghirlando, D.A.Torchia, and G.M.Clore (2011).
Atomic-resolution dynamics on the surface of amyloid-β protofibrils probed by solution NMR.
  Nature, 480, 268-272.  
21402079 O.Y.Ovchinnikova, V.H.Finder, I.Vodopivec, R.M.Nitsch, and R.Glockshuber (2011).
The Osaka FAD Mutation E22Δ Leads to the Formation of a Previously Unknown Type of Amyloid β Fibrils and Modulates Aβ Neurotoxicity.
  J Mol Biol, 408, 780-791.  
21487594 P.H.Nguyen, M.S.Li, and P.Derreumaux (2011).
Effects of all-atom force fields on amyloid oligomerization: replica exchange molecular dynamics simulations of the Aβ(16-22) dimer and trimer.
  Phys Chem Chem Phys, 13, 9778-9788.  
21279219 R.Mishra, D.Sjölander, and P.Hammarström (2011).
Spectroscopic characterization of diverse amyloid fibrils in vitro by the fluorescent dye Nile red.
  Mol Biosyst, 7, 1232-1240.  
21437790 S.Kumar, S.K.Singh, X.Wang, B.Rup, and D.Gill (2011).
Coupling of aggregation and immunogenicity in biotherapeutics: T- and B-cell immune epitopes may contain aggregation-prone regions.
  Pharm Res, 28, 949-961.  
21439479 T.Geppert, B.Hoy, S.Wessler, and G.Schneider (2011).
Context-based identification of protein-protein interfaces and "hot-spot" residues.
  Chem Biol, 18, 344-353.  
21287624 V.Babin, C.Roland, and C.Sagui (2011).
The α-sheet: A missing-in-action secondary structure?
  Proteins, 79, 937-946.  
20190788 A.Aguzzi, and T.O'Connor (2010).
Protein aggregation diseases: pathogenicity and therapeutic perspectives.
  Nat Rev Drug Discov, 9, 237-248.  
20409489 A.C.Brorsson, B.Bolognesi, G.G.Tartaglia, S.L.Shammas, G.Favrin, I.Watson, D.A.Lomas, F.Chiti, M.Vendruscolo, C.M.Dobson, D.C.Crowther, and L.M.Luheshi (2010).
Intrinsic determinants of neurotoxic aggregate formation by the amyloid beta peptide.
  Biophys J, 98, 1677-1684.  
20564554 A.Oda, K.Kobayashi, and O.Takahashi (2010).
Molecular-dynamics simulations for amyloid beta 1-42 monomer with D-aspartic acid residues using continuous solvent.
  Chem Biodivers, 7, 1357-1363.  
20032312 A.V.Kajava, U.Baxa, and A.C.Steven (2010).
Beta arcades: recurring motifs in naturally occurring and disease-related amyloid fibrils.
  FASEB J, 24, 1311-1319.  
20126745 C.Rodríguez-Rodríguez, A.Rimola, L.Rodríguez-Santiago, P.Ugliengo, A.Alvarez-Larena, H.Gutiérrez-de-Terán, M.Sodupe, and P.González-Duarte (2010).
Crystal structure of thioflavin-T and its binding to amyloid fibrils: insights at the molecular level.
  Chem Commun (Camb), 46, 1156-1158.  
20221247 C.Wu, M.T.Bowers, and J.E.Shea (2010).
Molecular structures of quiescently grown and brain-derived polymorphic fibrils of the Alzheimer amyloid abeta9-40 peptide: a comparison to agitated fibrils.
  PLoS Comput Biol, 6, e1000693.  
20049499 C.Yang, X.Zhu, J.Li, and R.Shi (2010).
Exploration of the mechanism for LPFFD inhibiting the formation of beta-sheet conformation of A beta(1-42) in water.
  J Mol Model, 16, 813-821.  
20302320 D.Jiang, X.Li, L.Liu, G.B.Yagnik, and F.Zhou (2010).
Reaction rates and mechanism of the ascorbic acid oxidation by molecular oxygen facilitated by Cu(II)-containing amyloid-beta complexes and aggregates.
  J Phys Chem B, 114, 4896-4903.  
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.  
20544966 H.Inouye, K.A.Gleason, D.Zhang, S.M.Decatur, and D.A.Kirschner (2010).
Differential effects of Phe19 and Phe20 on fibril formation by amyloidogenic peptide A beta 16-22 (Ac-KLVFFAE-NH2).
  Proteins, 78, 2306-2321.  
20308552 H.Jang, F.T.Arce, S.Ramachandran, R.Capone, R.Azimova, B.L.Kagan, R.Nussinov, and R.Lal (2010).
Truncated beta-amyloid peptide channels provide an alternative mechanism for Alzheimer's Disease and Down syndrome.
  Proc Natl Acad Sci U S A, 107, 6538-6543.  
20608696 H.Jang, F.Teran Arce, S.Ramachandran, R.Capone, R.Lal, and R.Nussinov (2010).
Structural convergence among diverse, toxic beta-sheet ion channels.
  J Phys Chem B, 114, 9445-9451.  
  19827141 H.Wu, A.Canfield, J.Adhikari, and S.Huo (2010).
Quantum mechanical studies on model alpha-pleated sheets.
  J Comput Chem, 31, 1216-1223.  
20106655 J.E.Straub, and D.Thirumalai (2010).
Principles governing oligomer formation in amyloidogenic peptides.
  Curr Opin Struct Biol, 20, 187-195.  
20931124 J.Geng, K.Qu, J.Ren, and X.Qu (2010).
Rapid and efficient screening of Alzheimer's disease β-amyloid inhibitors using label-free gold nanoparticles.
  Mol Biosyst, 6, 2389-2391.  
20593467 J.J.Bockhorn, K.L.Lazar, A.J.Gasser, L.M.Luther, I.M.Qahwash, N.Chopra, and S.C.Meredith (2010).
Novel semisynthetic method for generating full length beta-amyloid peptides.
  Biopolymers, 94, 511-520.  
20886513 J.Lindgren, A.Wahlström, J.Danielsson, N.Markova, C.Ekblad, A.Gräslund, L.Abrahmsén, A.E.Karlström, and S.K.Wärmländer (2010).
N-terminal engineering of amyloid-β-binding Affibody molecules yields improved chemical synthesis and higher binding affinity.
  Protein Sci, 19, 2319-2329.  
20422111 J.Shorter (2010).
Emergence and natural selection of drug-resistant prions.
  Mol Biosyst, 6, 1115-1130.  
20018889 J.W.Wu, L.Breydo, J.M.Isas, J.Lee, Y.G.Kuznetsov, R.Langen, and C.Glabe (2010).
Fibrillar oligomers nucleate the oligomerization of monomeric amyloid beta but do not seed fibril formation.
  J Biol Chem, 285, 6071-6079.  
19908073 K.Kassler, A.H.Horn, and H.Sticht (2010).
Effect of pathogenic mutations on the structure and dynamics of Alzheimer's A beta 42-amyloid oligomers.
  J Mol Model, 16, 1011-1020.  
20668734 K.Morris, and L.Serpell (2010).
From natural to designer self-assembling biopolymers, the structural characterisation of fibrous proteins & peptides using fibre diffraction.
  Chem Soc Rev, 39, 3445-3453.  
20196618 K.Numata, and D.L.Kaplan (2010).
Mechanisms of enzymatic degradation of amyloid Beta microfibrils generating nanofilaments and nanospheres related to cytotoxicity.
  Biochemistry, 49, 3254-3260.  
20714468 L.Niu, X.Ma, L.Liu, X.Mao, D.Wu, Y.Yang, Q.Zeng, and C.Wang (2010).
Molecularly tuned peptide assemblies at the liquid-solid interface studied by scanning tunneling microscopy.
  Phys Chem Chem Phys, 12, 11683-11687.  
20614050 L.Qin, J.Vastl, and J.Gao (2010).
Highly sensitive amyloid detection enabled by thioflavin T dimers.
  Mol Biosyst, 6, 1791-1795.  
20383142 M.Ahmed, J.Davis, D.Aucoin, T.Sato, S.Ahuja, S.Aimoto, J.I.Elliott, W.E.Van Nostrand, and S.O.Smith (2010).
Structural conversion of neurotoxic amyloid-beta(1-42) oligomers to fibrils.
  Nat Struct Mol Biol, 17, 561-567.  
20133689 M.Biancalana, K.Makabe, and S.Koide (2010).
Minimalist design of water-soluble cross-beta architecture.
  Proc Natl Acad Sci U S A, 107, 3469-3474.
PDB codes: 3cka 3eex
20694815 M.Gregori, V.Cassina, D.Brogioli, D.Salerno, L.De Kimpe, W.Scheper, M.Masserini, and F.Mantegazza (2010).
Stability of Aβ (1-42) peptide fibrils as consequence of environmental modifications.
  Eur Biophys J, 39, 1613-1623.  
20977664 M.Stefani (2010).
Biochemical and biophysical features of both oligomer/fibril and cell membrane in amyloid cytotoxicity.
  FEBS J, 277, 4602-4613.  
20338850 N.Blinov, L.Dorosh, D.Wishart, and A.Kovalenko (2010).
Association thermodynamics and conformational stability of beta-sheet amyloid beta(17-42) oligomers: effects of E22Q (Dutch) mutation and charge neutralization.
  Biophys J, 98, 282-296.  
20669960 O.Khakshoor, A.J.Lin, T.P.Korman, M.R.Sawaya, S.C.Tsai, D.Eisenberg, and J.S.Nowick (2010).
X-ray crystallographic structure of an artificial beta-sheet dimer.
  J Am Chem Soc, 132, 11622-11628.
PDB code: 3ni3
21144050 R.Kayed, I.Canto, L.Breydo, S.Rasool, T.Lukacsovich, J.Wu, R.Albay, A.Pensalfini, S.Yeung, E.Head, J.L.Marsh, and C.Glabe (2010).
Conformation dependent monoclonal antibodies distinguish different replicating strains or conformers of prefibrillar Aβ oligomers.
  Mol Neurodegener, 5, 57.  
21479077 R.Owenius, A.Jarl, B.H.Jonsson, U.Carlsson, and P.Hammarström (2010).
GroEL-induced topological dislocation of a substrate protein β-sheet core: a solution EPR spin-spin distance study.
  J Chem Biol, 3, 127-139.  
20133839 R.P.Friedrich, K.Tepper, R.Rönicke, M.Soom, M.Westermann, K.Reymann, C.Kaether, and M.Fändrich (2010).
Mechanism of amyloid plaque formation suggests an intracellular basis of Abeta pathogenicity.
  Proc Natl Acad Sci U S A, 107, 1942-1947.  
20550420 S.Kim, T.Takeda, and D.K.Klimov (2010).
Globular state in the oligomers formed by Abeta peptides.
  J Chem Phys, 132, 225101.  
20302321 T.Takeda, and D.K.Klimov (2010).
Computational backbone mutagenesis of Abeta peptides: probing the role of backbone hydrogen bonds in aggregation.
  J Phys Chem B, 114, 4755-4762.  
20635343 T.Takeda, W.E.Chang, E.P.Raman, and D.K.Klimov (2010).
Binding of nonsteroidal anti-inflammatory drugs to Abeta fibril.
  Proteins, 78, 2849-2860.  
20798063 W.Zhuang, N.G.Sgourakis, Z.Li, A.E.Garcia, and S.Mukamel (2010).
Discriminating early stage A{beta}42 monomer structures using chirality-induced 2DIR spectroscopy in a simulation study.
  Proc Natl Acad Sci U S A, 107, 15687-15692.  
21031399 Y.Hu, B.Su, C.S.Kim, M.Hernandez, A.Rostagno, J.Ghiso, and J.R.Kim (2010).
A strategy for designing a peptide probe for detection of β-amyloid oligomers.
  Chembiochem, 11, 2409-2418.  
20660780 Y.Miller, B.Ma, C.J.Tsai, and R.Nussinov (2010).
Hollow core of Alzheimer's Abeta42 amyloid observed by cryoEM is relevant at physiological pH.
  Proc Natl Acad Sci U S A, 107, 14128-14133.  
20402519 Y.Miller, B.Ma, and R.Nussinov (2010).
Polymorphism in Alzheimer Abeta amyloid organization reflects conformational selection in a rugged energy landscape.
  Chem Rev, 110, 4820-4838.  
20448202 Y.Miller, B.Ma, and R.Nussinov (2010).
Zinc ions promote Alzheimer Abeta aggregation via population shift of polymorphic states.
  Proc Natl Acad Sci U S A, 107, 9490-9495.  
20939098 Y.Shafrir, S.Durell, N.Arispe, and H.R.Guy (2010).
Models of membrane-bound Alzheimer's Abeta peptide assemblies.
  Proteins, 78, 3473-3487.  
19376973 A.K.Paravastu, I.Qahwash, R.D.Leapman, S.C.Meredith, and R.Tycko (2009).
Seeded growth of beta-amyloid fibrils from Alzheimer's brain-derived fibrils produces a distinct fibril structure.
  Proc Natl Acad Sci U S A, 106, 7443-7448.  
19549187 A.Olofsson, M.Lindhagen-Persson, M.Vestling, A.E.Sauer-Eriksson, and A.Ohman (2009).
Quenched hydrogen/deuterium exchange NMR characterization of amyloid-beta peptide aggregates formed in the presence of Cu2+ or Zn2+.
  FEBS J, 276, 4051-4060.  
19690748 A.Rauk (2009).
The chemistry of Alzheimer's disease.
  Chem Soc Rev, 38, 2698-2715.  
19325876 A.W.Bryan, M.Menke, L.J.Cowen, S.L.Lindquist, and B.Berger (2009).
BETASCAN: probable beta-amyloids identified by pairwise probabilistic analysis.
  PLoS Comput Biol, 5, e1000333.  
19186145 A.Zhang, W.Qi, T.A.Good, and E.J.Fernandez (2009).
Structural differences between Abeta(1-40) intermediate oligomers and fibrils elucidated by proteolytic fragmentation and hydrogen/deuterium exchange.
  Biophys J, 96, 1091-1104.  
19231987 B.Caughey, G.S.Baron, B.Chesebro, and M.Jeffrey (2009).
Getting a grip on prions: oligomers, amyloids, and pathological membrane interactions.
  Annu Rev Biochem, 78, 177-204.  
19186121 C.H.Davis, and M.L.Berkowitz (2009).
Interaction between amyloid-beta (1-42) peptide and phospholipid bilayers: a molecular dynamics study.
  Biophys J, 96, 785-797.  
19373825 C.L.Sun, X.N.Jiang, and C.S.Wang (2009).
An analytic potential energy function for the amide-amide and amide-water intermolecular hydrogen bonds in peptides.
  J Comput Chem, 30, 2567-2575.  
19458258 C.Nerelius, A.Sandegren, H.Sargsyan, R.Raunak, H.Leijonmarck, U.Chatterjee, A.Fisahn, S.Imarisio, D.A.Lomas, D.C.Crowther, R.Strömberg, and J.Johansson (2009).
Alpha-helix targeting reduces amyloid-beta peptide toxicity.
  Proc Natl Acad Sci U S A, 106, 9191-9196.  
19030989 C.Rivière, J.C.Delaunay, F.Immel, C.Cullin, and J.P.Monti (2009).
The polyphenol piceid destabilizes preformed amyloid fibrils and oligomers in vitro: hypothesis on possible molecular mechanisms.
  Neurochem Res, 34, 1120-1128.  
19540126 D.Chen, Z.S.Martin, C.Soto, and C.H.Schein (2009).
Computational selection of inhibitors of Abeta aggregation and neuronal toxicity.
  Bioorg Med Chem, 17, 5189-5197.  
19591190 D.Grillo-Bosch, N.Carulla, M.Cruz, L.Sánchez, R.Pujol-Pina, S.Madurga, F.Rabanal, and E.Giralt (2009).
Retro-enantio N-methylated peptides as beta-amyloid aggregation inhibitors.
  ChemMedChem, 4, 1488-1494.  
19435461 E.Cerf, R.Sarroukh, S.Tamamizu-Kato, L.Breydo, S.Derclaye, Y.F.Dufrêne, V.Narayanaswami, E.Goormaghtigh, J.M.Ruysschaert, and V.Raussens (2009).
Antiparallel beta-sheet: a signature structure of the oligomeric amyloid beta-peptide.
  Biochem J, 421, 415-423.  
19804739 E.P.Raman, T.Takeda, and D.K.Klimov (2009).
Molecular dynamics simulations of Ibuprofen binding to Abeta peptides.
  Biophys J, 97, 2070-2079.  
19651050 H.Ding, P.T.Wong, E.L.Lee, A.Gafni, and D.G.Steel (2009).
Determination of the oligomer size of amyloidogenic protein beta-amyloid(1-40) by single-molecule spectroscopy.
  Biophys J, 97, 912-921.  
19948133 H.Jang, F.T.Arce, R.Capone, S.Ramachandran, R.Lal, and R.Nussinov (2009).
Misfolded amyloid ion channels present mobile beta-sheet subunits in contrast to conventional ion channels.
  Biophys J, 97, 3029-3037.  
  19946595 I.Sepkhanova, M.Drescher, N.J.Meeuwenoord, R.W.Limpens, R.I.Koning, D.V.Filippov, and M.Huber (2009).
Monitoring Alzheimer Amyloid Peptide Aggregation by EPR.
  Appl Magn Reson, 36, 209-222.  
19621381 I.T.Yonemoto, M.R.Wood, W.E.Balch, and J.W.Kelly (2009).
A general strategy for the bacterial expression of amyloidogenic peptides using BCL-XL-1/2 fusions.
  Protein Sci, 18, 1978-1986.  
19416063 J.A.Hebda, and A.D.Miranker (2009).
The interplay of catalysis and toxicity by amyloid intermediates on lipid bilayers: insights from type II diabetes.
  Annu Rev Biophys, 38, 125-152.  
20006956 J.H.Choi, B.C.May, H.Wille, and F.E.Cohen (2009).
Molecular modeling of the misfolded insulin subunit and amyloid fibril.
  Biophys J, 97, 3187-3195.  
19009593 J.Lee, S.Ham, and W.Im (2009).
Beta-hairpin restraint potentials for calculations of potentials of mean force as a function of beta-hairpin tilt, rotation, and distance.
  J Comput Chem, 30, 1334-1343.  
19301007 J.Meinhardt, and M.Fändrich (2009).
[Structure of amyloid fibrils]
  Pathologe, 30, 175-181.  
19730673 J.Park, B.Kahng, and W.Hwang (2009).
Thermodynamic selection of steric zipper patterns in the amyloid cross-beta spine.
  PLoS Comput Biol, 5, e1000492.  
19841277 K.Usui, J.D.Hulleman, J.F.Paulsson, S.J.Siegel, E.T.Powers, and J.W.Kelly (2009).
Site-specific modification of Alzheimer's peptides by cholesterol oxidation products enhances aggregation energetics and neurotoxicity.
  Proc Natl Acad Sci U S A, 106, 18563-18568.  
19450500 L.Qiu, A.Lewis, J.Como, M.W.Vaughn, J.Huang, P.Somerharju, J.Virtanen, and K.H.Cheng (2009).
Cholesterol modulates the interaction of beta-amyloid peptide with lipid bilayers.
  Biophys J, 96, 4299-4307.  
  19806034 L.Wang (2009).
Towards revealing the structure of bacterial inclusion bodies.
  Prion, 3, 139-145.  
19038267 M.Biancalana, K.Makabe, A.Koide, and S.Koide (2009).
Molecular mechanism of thioflavin-T binding to the surface of beta-rich peptide self-assemblies.
  J Mol Biol, 385, 1052-1063.
PDB code: 3ec5
19388095 M.D.Meadowcroft, J.R.Connor, M.B.Smith, and Q.X.Yang (2009).
MRI and histological analysis of beta-amyloid plaques in both human Alzheimer's disease and APP/PS1 transgenic mice.
  J Magn Reson Imaging, 29, 997.  
  19597329 M.Fändrich, J.Meinhardt, and N.Grigorieff (2009).
Structural polymorphism of Alzheimer Abeta and other amyloid fibrils.
  Prion, 3, 89-93.  
19652839 M.Fernando Cobo, K.Malináková, D.Reichert, K.Saalwächter, and E.Ribeiro Deazevedo (2009).
Intermediate motions and dipolar couplings as studied by Lee-Goldburg cross-polarization NMR: Hartmann-Hahn matching profiles.
  Phys Chem Chem Phys, 11, 7036-7047.  
19838688 M.Ionuţ Iuraşcu, C.Cozma, N.Tomczyk, J.Rontree, M.Desor, M.Drescher, and M.Przybylski (2009).
Structural characterization of beta-amyloid oligomer-aggregates by ion mobility mass spectrometry and electron spin resonance spectroscopy.
  Anal Bioanal Chem, 395, 2509-2519.  
19824733 M.Mustata, R.Capone, H.Jang, F.T.Arce, S.Ramachandran, R.Lal, and R.Nussinov (2009).
K3 fragment of amyloidogenic beta(2)-microglobulin forms ion channels: implication for dialysis related amyloidosis.
  J Am Chem Soc, 131, 14938-14945.  
19843697 M.Schmidt, C.Sachse, W.Richter, C.Xu, M.Fändrich, and N.Grigorieff (2009).
Comparison of Alzheimer Abeta(1-40) and Abeta(1-42) amyloid fibrils reveals similar protofilament structures.
  Proc Natl Acad Sci U S A, 106, 19813-19818.  
19416886 N.Carulla, M.Zhou, M.Arimon, M.Gairí, E.Giralt, C.V.Robinson, and C.M.Dobson (2009).
Experimental characterization of disordered and ordered aggregates populated during the process of amyloid fibril formation.
  Proc Natl Acad Sci U S A, 106, 7828-7833.  
19995075 N.Miyashita, J.E.Straub, and D.Thirumalai (2009).
Structures of beta-amyloid peptide 1-40, 1-42, and 1-55-the 672-726 fragment of APP-in a membrane environment with implications for interactions with gamma-secretase.
  J Am Chem Soc, 131, 17843-17852.  
19767826 P.E.Arslan, and A.Chakrabartty (2009).
Probing Alzheimer amyloid peptide aggregation using a cell-free fluorescent protein refolding method.
  Biochem Cell Biol, 87, 631-639.  
19602569 P.K.Teng, and D.Eisenberg (2009).
Short protein segments can drive a non-fibrillizing protein into the amyloid state.
  Protein Eng Des Sel, 22, 531-536.  
19450490 P.Picone, R.Carrotta, G.Montana, M.R.Nobile, P.L.San Biagio, and M.Di Carlo (2009).
Abeta oligomers and fibrillar aggregates induce different apoptotic pathways in LAN5 neuroblastoma cell cultures.
  Biophys J, 96, 4200-4211.  
19712107 P.Tompa (2009).
Structural disorder in amyloid fibrils: its implication in dynamic interactions of proteins.
  FEBS J, 276, 5406-5415.  
19995078 R.P.Nanga, J.R.Brender, S.Vivekanandan, N.Popovych, and A.Ramamoorthy (2009).
NMR structure in a membrane environment reveals putative amyloidogenic regions of the SEVI precursor peptide PAP(248-286).
  J Am Chem Soc, 131, 17972-17979.
PDB code: 2l3h
19304665 R.S.Boshuizen, V.Schulz, M.Morbin, G.Mazzoleni, R.H.Meloen, and J.P.Langedijk (2009).
Heterologous stacking of prion protein peptides reveals structural details of fibrils and facilitates complete inhibition of fibril growth.
  J Biol Chem, 284, 12809-12820.  
19264960 R.Zhang, X.Hu, H.Khant, S.J.Ludtke, W.Chiu, M.F.Schmid, C.Frieden, and J.M.Lee (2009).
Interprotofilament interactions between Alzheimer's Abeta1-42 peptides in amyloid fibrils revealed by cryoEM.
  Proc Natl Acad Sci U S A, 106, 4653-4658.  
19244249 S.M.Patil, S.Xu, S.R.Sheftic, and A.T.Alexandrescu (2009).
Dynamic alpha-helix structure of micelle-bound human amylin.
  J Biol Chem, 284, 11982-11991.
PDB code: 2kb8
19350616 T.Takeda, and D.K.Klimov (2009).
Interpeptide interactions induce helix to strand structural transition in Abeta peptides.
  Proteins, 77, 1.  
19167295 T.Takeda, and D.K.Klimov (2009).
Replica exchange simulations of the thermodynamics of Abeta fibril growth.
  Biophys J, 96, 442-452.  
19419218 T.Takeda, and D.K.Klimov (2009).
Probing the effect of amino-terminal truncation for Abeta1-40 peptides.
  J Phys Chem B, 113, 6692-6702.  
19486667 T.Takeda, and D.K.Klimov (2009).
Probing energetics of Abeta fibril elongation by molecular dynamics simulations.
  Biophys J, 96, 4428-4437.  
19708712 T.Takeda, and D.K.Klimov (2009).
Side chain interactions can impede amyloid fibril growth: replica exchange simulations of Abeta peptide mutant.
  J Phys Chem B, 113, 11848-11857.  
19383476 T.Zako, M.Sakono, N.Hashimoto, M.Ihara, and M.Maeda (2009).
Bovine insulin filaments induced by reducing disulfide bonds show a different morphology, secondary structure, and cell toxicity from intact insulin amyloid fibrils.
  Biophys J, 96, 3331-3340.  
  19885010 Y.H.Park, Y.J.Kim, I.H.Son, and H.D.Yang (2009).
Inhibition of beta-amyloid(1-40) Peptide Aggregation and Neurotoxicity by Citrate.
  Korean J Physiol Pharmacol, 13, 273-279.  
19115328 Y.Masuda, S.Uemura, R.Ohashi, A.Nakanishi, K.Takegoshi, T.Shimizu, T.Shirasawa, and K.Irie (2009).
Identification of physiological and toxic conformations in abeta42 aggregates.
  Chembiochem, 10, 287-295.  
19686665 Y.Miller, B.Ma, and R.Nussinov (2009).
Polymorphism of Alzheimer's Abeta17-42 (p3) oligomers: the importance of the turn location and its conformation.
  Biophys J, 97, 1168-1177.  
19905362 Y.Mu, and Y.Q.Gao (2009).
Self-assembly of polypeptides into left-handedly twisted fibril-like structures.
  Phys Rev E Stat Nonlin Soft Matter Phys, 80, 041927.  
19815514 Y.S.Kim, L.Liu, P.H.Axelsen, and R.M.Hochstrasser (2009).
2D IR provides evidence for mobile water molecules in beta-amyloid fibrils.
  Proc Natl Acad Sci U S A, 106, 17751-17756.  
19751686 Z.Fu, Y.Luo, P.Derreumaux, and G.Wei (2009).
Induced beta-barrel formation of the Alzheimer's Abeta25-35 oligomers on carbon nanotube surfaces: implication for amyloid fibril inhibition.
  Biophys J, 97, 1795-1803.  
18283694 A.Hetényi, L.Fülöp, T.A.Martinek, E.Wéber, K.Soós, and B.Penke (2008).
Ligand-induced flocculation of neurotoxic fibrillar Abeta(1-42) by noncovalent crosslinking.
  Chembiochem, 9, 748-757.  
17932914 A.Irbäck, and S.Mitternacht (2008).
Spontaneous beta-barrel formation: an all-atom Monte Carlo study of Abeta16-22 oligomerization.
  Proteins, 71, 207-214.  
18305836 A.Rauk (2008).
Why is the amyloid beta peptide of Alzheimer's disease neurotoxic?
  Dalton Trans, (), 1273-1282.  
18973685 B.Macao, W.Hoyer, A.Sandberg, A.C.Brorsson, C.M.Dobson, and T.Härd (2008).
Recombinant amyloid beta-peptide production by coexpression with an affibody ligand.
  BMC Biotechnol, 8, 82.  
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.
  J Mol Biol, 379, 815-829.  
18723507 C.G.Glabe (2008).
Structural classification of toxic amyloid oligomers.
  J Biol Chem, 283, 29639-29643.  
18408040 C.Liang, P.Derreumaux, N.Mousseau, and G.Wei (2008).
The beta-strand-loop-beta-strand conformation is marginally populated in beta2-microglobulin (20-41) peptide in solution as revealed by replica exchange molecular dynamics simulations.
  Biophys J, 95, 510-517.  
18483195 C.Sachse, M.Fändrich, and N.Grigorieff (2008).
Paired beta-sheet structure of an Abeta(1-40) amyloid fibril revealed by electron microscopy.
  Proc Natl Acad Sci U S A, 105, 7462-7466.  
18058241 E.Nordling, Y.Kallberg, J.Johansson, and B.Persson (2008).
Molecular dynamics studies of alpha-helix stability in fibril-forming peptides.
  J Comput Aided Mol Des, 22, 53-58.  
18420597 G.Aoki, T.K.Yamada, M.Arii, S.Kojima, and T.Mizoguchi (2008).
Requirement of Ala residues at g position in heptad sequence of alpha-helix-forming peptide for formation of fibrous structure.
  J Biochem, 144, 15-19.  
18568165 G.G.Tartaglia, and M.Vendruscolo (2008).
The Zyggregator method for predicting protein aggregation propensities.
  Chem Soc Rev, 37, 1395-1401.  
18515395 G.Valincius, F.Heinrich, R.Budvytyte, D.J.Vanderah, D.J.McGillivray, Y.Sokolov, J.E.Hall, and M.Lösche (2008).
Soluble amyloid beta-oligomers affect dielectric membrane properties by bilayer insertion and domain formation: implications for cell toxicity.
  Biophys J, 95, 4845-4861.  
18161737 H.Heise (2008).
Solid-state NMR spectroscopy of amyloid proteins.
  Chembiochem, 9, 179-189.  
18182298 H.Jang, J.Zheng, R.Lal, and R.Nussinov (2008).
New structures help the modeling of toxic amyloidbeta ion channels.
  Trends Biochem Sci, 33, 91.  
18480256 H.Wang, M.L.Duennwald, B.E.Roberts, L.M.Rozeboom, Y.L.Zhang, A.D.Steele, R.Krishnan, L.J.Su, D.Griffin, S.Mukhopadhyay, E.J.Hennessy, P.Weigele, B.J.Blanchard, J.King, A.A.Deniz, S.L.Buchwald, V.M.Ingram, S.Lindquist, and J.Shorter (2008).
Direct and selective elimination of specific prions and amyloids by 4,5-dianilinophthalimide and analogs.
  Proc Natl Acad Sci U S A, 105, 7159-7164.  
18085519 I.Y.Toropygin, E.V.Kugaevskaya, O.A.Mirgorodskaya, Y.E.Elisseeva, Y.P.Kozmin, I.A.Popov, E.N.Nikolaev, A.A.Makarov, and S.A.Kozin (2008).
The N-domain of angiotensin-converting enzyme specifically hydrolyzes the Arg-5-His-6 bond of Alzheimer's Abeta-(1-16) peptide and its isoAsp-7 analogue with different efficiency as evidenced by quantitative matrix-assisted laser desorption/ionization time-of-flight mass spectrometry.
  Rapid Commun Mass Spectrom, 22, 231-239.  
18642254 J.Becker, N.Ferguson, J.Flinders, B.J.van Rossum, A.R.Fersht, and H.Oschkinat (2008).
A sequential assignment procedure for proteins that have intermediate line widths in MAS NMR spectra: amyloid fibrils of human CA150.WW2.
  Chembiochem, 9, 1946-1952.  
  19812735 J.H.Zhao, H.L.Liu, H.Y.Lin, C.H.Huang, H.W.Fang, S.S.Chen, Y.Ho, W.B.Tsai, and W.Y.Chen (2008).
Chemical chaperone and inhibitor discovery: potential treatments for protein conformational diseases.
  Perspect Medicin Chem, 1, 39-48.  
18436646 J.J.Helmus, K.Surewicz, P.S.Nadaud, W.K.Surewicz, and C.P.Jaroniec (2008).
Molecular conformation and dynamics of the Y145Stop variant of human prion protein in amyloid fibrils.
  Proc Natl Acad Sci U S A, 105, 6284-6289.  
18262468 J.P.Changeux, and A.Taly (2008).
Nicotinic receptors, allosteric proteins and medicine.
  Trends Mol Med, 14, 93.  
19090986 J.R.Cashman, S.Ghirmai, K.J.Abel, and M.Fiala (2008).
Immune defects in Alzheimer's disease: new medications development.
  BMC Neurosci, 9, S13.  
18457440 J.Zheng, H.Jang, B.Ma, and R.Nussinov (2008).
Annular structures as intermediates in fibril formation of Alzheimer Abeta17-42.
  J Phys Chem B, 112, 6856-6865.  
  19098440 K.C.Kunes, S.C.Clark, D.L.Cox, and R.R.Singh (2008).
Left handed beta helix models for mammalian prion fibrils.
  Prion, 2, 81-90.  
18367205 K.Makabe, M.Biancalana, S.Yan, V.Tereshko, G.Gawlak, H.Miller-Auer, S.C.Meredith, and S.Koide (2008).
High-resolution structure of a self-assembly-competent form of a hydrophobic peptide captured in a soluble beta-sheet scaffold.
  J Mol Biol, 378, 459-467.
PDB code: 2i5v
18250627 K.U.Wendt, M.S.Weiss, P.Cramer, and D.W.Heinz (2008).
Structures and diseases.
  Nat Struct Mol Biol, 15, 117-120.  
18684013 L.Wang, S.K.Maji, M.R.Sawaya, D.Eisenberg, and R.Riek (2008).
Bacterial inclusion bodies contain amyloid-like structure.
  PLoS Biol, 6, e195.  
18597778 M.G.Krone, A.Baumketner, S.L.Bernstein, T.Wyttenbach, N.D.Lazo, D.B.Teplow, M.T.Bowers, and J.E.Shea (2008).
Effects of familial Alzheimer's disease mutations on the folding nucleation of the amyloid beta-protein.
  J Mol Biol, 381, 221-228.  
18550842 M.Vilar, H.T.Chou, T.Lührs, S.K.Maji, D.Riek-Loher, R.Verel, G.Manning, H.Stahlberg, and R.Riek (2008).
The fold of alpha-synuclein fibrils.
  Proc Natl Acad Sci U S A, 105, 8637-8642.  
18835397 M.Yang, and D.B.Teplow (2008).
Amyloid beta-protein monomer folding: free-energy surfaces reveal alloform-specific differences.
  J Mol Biol, 384, 450-464.  
18646868 N.L.Fawzi, E.H.Yap, Y.Okabe, K.L.Kohlstedt, S.P.Brown, and T.Head-Gordon (2008).
Contrasting disease and nondisease protein aggregation by molecular simulation.
  Acc Chem Res, 41, 1037-1047.  
19063575 N.W.Kelley, V.Vishal, G.A.Krafft, and V.S.Pande (2008).
Simulating oligomerization at experimental concentrations and long timescales: A Markov state model approach.
  J Chem Phys, 129, 214707.  
  19158505 R.N.Rambaran, and L.C.Serpell (2008).
Amyloid fibrils: abnormal protein assembly.
  Prion, 2, 112-117.  
17588526 T.R.Jahn, and S.E.Radford (2008).
Folding versus aggregation: polypeptide conformations on competing pathways.
  Arch Biochem Biophys, 469, 100-117.  
18502791 T.Takeda, and D.K.Klimov (2008).
Temperature-induced dissociation of Abeta monomers from amyloid fibril.
  Biophys J, 95, 1758-1772.  
18689456 T.Yamazaki, N.Blinov, D.Wishart, and A.Kovalenko (2008).
Hydration effects on the HET-s prion and amyloid-beta fibrillous aggregates, studied with three-dimensional molecular theory of solvation.
  Biophys J, 95, 4540-4548.  
18537545 U.Baxa (2008).
Structural basis of infectious and non-infectious amyloids.
  Curr Alzheimer Res, 5, 308-318.  
18599641 V.A.Streltsov, S.J.Titmuss, V.C.Epa, K.J.Barnham, C.L.Masters, and J.N.Varghese (2008).
The structure of the amyloid-beta peptide high-affinity copper II binding site in Alzheimer disease.
  Biophys J, 95, 3447-3456.  
18004559 V.Streltsov (2008).
X-ray absorption and diffraction studies of the metal binding sites in amyloid beta-peptide.
  Eur Biophys J, 37, 257-263.  
18375754 W.Hoyer, C.Grönwall, A.Jonsson, S.Ståhl, and T.Härd (2008).
Stabilization of a beta-hairpin in monomeric Alzheimer's amyloid-beta peptide inhibits amyloid formation.
  Proc Natl Acad Sci U S A, 105, 5099-5104.
PDB code: 2otk
18258258 W.Kim, and M.H.Hecht (2008).
Mutations enhance the aggregation propensity of the Alzheimer's A beta peptide.
  J Mol Biol, 377, 565-574.  
18376983 X.Dong, W.Chen, N.Mousseau, and P.Derreumaux (2008).
Energy landscapes of the monomer and dimer of the Alzheimer's peptide Abeta(1-28).
  J Chem Phys, 128, 125108.  
18565345 X.Wang, and M.R.Chapman (2008).
Sequence determinants of bacterial amyloid formation.
  J Mol Biol, 380, 570-580.  
18499799 Y.S.Kim, L.Liu, P.H.Axelsen, and R.M.Hochstrasser (2008).
Two-dimensional infrared spectra of isotopically diluted amyloid fibrils from Abeta40.
  Proc Natl Acad Sci U S A, 105, 7720-7725.  
17718715 A.A.Reinke, and J.E.Gestwicki (2007).
Structure-activity relationships of amyloid beta-aggregation inhibitors based on curcumin: influence of linker length and flexibility.
  Chem Biol Drug Des, 70, 206-215.  
17767153 B.H.Toyama, M.J.Kelly, J.D.Gross, and J.S.Weissman (2007).
The structural basis of yeast prion strain variants.
  Nature, 449, 233-237.  
17962399 C.Frieden (2007).
Protein aggregation processes: In search of the mechanism.
  Protein Sci, 16, 2334-2344.  
17412596 D.M.Fowler, A.V.Koulov, W.E.Balch, and J.W.Kelly (2007).
Functional amyloid--from bacteria to humans.
  Trends Biochem Sci, 32, 217-224.  
17211889 F.Dulin, I.Callebaut, N.Colloc'h, and J.P.Mornon (2007).
Sequence-based modeling of Abeta42 soluble oligomers.
  Biopolymers, 85, 422-437.  
17206626 G.Tuchscherer, A.Chandravarkar, M.S.Camus, J.Bérard, K.Murat, A.Schmid, R.Mimna, H.A.Lashuel, and M.Mutter (2007).
Switch-peptides as folding precursors in self-assembling peptides and amyloid fibrillogenesis.
  Biopolymers, 88, 239-252.  
  19164927 G.Wei, N.Mousseau, and P.Derreumaux (2007).
Computational simulations of the early steps of protein aggregation.
  Prion, 1, 3-8.  
17526580 H.Jang, J.Zheng, and R.Nussinov (2007).
Models of beta-amyloid ion channels in the membrane suggest that channel formation in the bilayer is a dynamic process.
  Biophys J, 93, 1938-1949.  
17701466 H.LeVine (2007).
Small molecule inhibitors of Abeta assembly.
  Amyloid, 14, 185-197.  
17212510 J.H.Meinke, and U.H.Hansmann (2007).
Aggregation of beta-amyloid fragments.
  J Chem Phys, 126, 014706.  
17656579 J.Ikebe, N.Kamiya, J.Ito, H.Shindo, and J.Higo (2007).
Simulation study on the disordered state of an Alzheimer's beta amyloid peptide Abeta(12 36) in water consisting of random-structural, beta-structural, and helical clusters.
  Protein Sci, 16, 1596-1608.  
17942695 J.Khandogin, and C.L.Brooks (2007).
Linking folding with aggregation in Alzheimer's beta-amyloid peptides.
  Proc Natl Acad Sci U S A, 104, 16880-16885.  
17675353 J.Zheng, H.Jang, B.Ma, C.J.Tsai, and R.Nussinov (2007).
Modeling the Alzheimer Abeta17-42 fibril architecture: tight intermolecular sheet-sheet association and intramolecular hydrated cavities.
  Biophys J, 93, 3046-3057.  
17114229 J.van Gestel, and S.W.de Leeuw (2007).
The formation of fibrils by intertwining of filaments: model and application to amyloid Abeta protein.
  Biophys J, 92, 1157-1163.  
17549789 K.H.Lim, G.L.Henderson, A.Jha, and M.Louhivuori (2007).
Structural, dynamic properties of key residues in Abeta amyloidogenesis: implications of an important role of nanosecond timescale dynamics.
  Chembiochem, 8, 1251-1254.  
17716740 M.A.Findeis (2007).
The role of amyloid beta peptide 42 in Alzheimer's disease.
  Pharmacol Ther, 116, 266-286.  
17940047 M.A.Grant, N.D.Lazo, A.Lomakin, M.M.Condron, H.Arai, G.Yamin, A.C.Rigby, and D.B.Teplow (2007).
Familial Alzheimer's disease mutations alter the stability of the amyloid beta-protein monomer folding nucleus.
  Proc Natl Acad Sci U S A, 104, 16522-16527.  
17652175 M.Fiala, P.T.Liu, A.Espinosa-Jeffrey, M.J.Rosenthal, G.Bernard, J.M.Ringman, J.Sayre, L.Zhang, J.Zaghi, S.Dejbakhsh, B.Chiang, J.Hui, M.Mahanian, A.Baghaee, P.Hong, and J.Cashman (2007).
Innate immunity and transcription of MGAT-III and Toll-like receptors in Alzheimer's disease patients are improved by bisdemethoxycurcumin.
  Proc Natl Acad Sci U S A, 104, 12849-12854.  
17468747 M.R.Sawaya, S.Sambashivan, R.Nelson, M.I.Ivanova, S.A.Sievers, M.I.Apostol, M.J.Thompson, M.Balbirnie, J.J.Wiltzius, H.T.McFarlane, A...Madsen, C.Riekel, and D.Eisenberg (2007).
Atomic structures of amyloid cross-beta spines reveal varied steric zippers.
  Nature, 447, 453-457.
PDB codes: 2okz 2ol9 2olx 2omm 2omp 2omq 2on9 2ona 2onv 2onw 2onx
17397862 N.G.Sgourakis, Y.Yan, S.A.McCallum, C.Wang, and A.E.Garcia (2007).
The Alzheimer's peptides Abeta40 and 42 adopt distinct conformations in water: a combined MD / NMR study.
  J Mol Biol, 368, 1448-1457.  
17416628 N.Haspel, D.Zanuy, J.Zheng, C.Aleman, H.Wolfson, and R.Nussinov (2007).
Changing the charge distribution of beta-helical-based nanostructures can provide the conditions for charge transfer.
  Biophys J, 93, 245-253.  
18025469 N.J.Cobb, F.D.Sönnichsen, H.McHaourab, and W.K.Surewicz (2007).
Molecular architecture of human prion protein amyloid: a parallel, in-register beta-structure.
  Proc Natl Acad Sci U S A, 104, 18946-18951.  
17912257 N.J.Cobb, and W.K.Surewicz (2007).
Prion strains under the magnifying glass.
  Nat Struct Mol Biol, 14, 882-884.  
17070840 N.L.Fawzi, Y.Okabe, E.H.Yap, and T.Head-Gordon (2007).
Determining the critical nucleus and mechanism of fibril elongation of the Alzheimer's Abeta(1-40) peptide.
  J Mol Biol, 365, 535-550.  
17198370 R.Wetzel, S.Shivaprasad, and A.D.Williams (2007).
Plasticity of amyloid fibrils.
  Biochemistry, 46, 1.  
17091525 S.Jaroch (2007).
A Soluble Amyloid Fibril Segment to Study Aggregate Formation.
  ChemMedChem, 2, 47-49.  
17497676 S.R.Leliveld, and C.Korth (2007).
The use of conformation-specific ligands and assays to dissect the molecular mechanisms of neurodegenerative diseases.
  J Neurosci Res, 85, 2285-2297.  
17368671 S.Wallin, K.B.Zeldovich, and E.I.Shakhnovich (2007).
The folding mechanics of a knotted protein.
  J Mol Biol, 368, 884-893.  
17456743 S.Zibaee, O.S.Makin, M.Goedert, and L.C.Serpell (2007).
A simple algorithm locates beta-strands in the amyloid fibril core of alpha-synuclein, Abeta, and tau using the amino acid sequence alone.
  Protein Sci, 16, 906-918.  
17925444 T.Ackbarow, X.Chen, S.Keten, and M.J.Buehler (2007).
Hierarchies, multiple energy barriers, and robustness govern the fracture mechanics of alpha-helical and beta-sheet protein domains.
  Proc Natl Acad Sci U S A, 104, 16410-16415.  
18096801 T.P.Knowles, A.W.Fitzpatrick, S.Meehan, H.R.Mott, M.Vendruscolo, C.M.Dobson, and M.E.Welland (2007).
Role of intermolecular forces in defining material properties of protein nanofibrils.
  Science, 318, 1900-1903.  
17503423 T.Takahashi, K.Ohta, and H.Mihara (2007).
Embedding the amyloid beta-peptide sequence in green fluorescent protein inhibits Abeta oligomerization.
  Chembiochem, 8, 985-988.  
17976024 V.N.Uversky (2007).
Nanoimaging in protein-misfolding and -conformational diseases.
  Nanomed, 2, 615-643.  
17675411 W.Zhuang, D.Abramavicius, D.V.Voronine, and S.Mukamel (2007).
Simulation of two-dimensional infrared spectroscopy of amyloid fibrils.
  Proc Natl Acad Sci U S A, 104, 14233-14236.  
17483185 Z.Zhang, H.Chen, H.Bai, and L.Lai (2007).
Molecular dynamics simulations on the oligomer-formation process of the GNNQQNY peptide from yeast prion protein Sup35.
  Biophys J, 93, 1484-1492.  
16731963 A.Baumketner, S.L.Bernstein, T.Wyttenbach, N.D.Lazo, D.B.Teplow, M.T.Bowers, and J.E.Shea (2006).
Structure of the 21-30 fragment of amyloid beta-protein.
  Protein Sci, 15, 1239-1247.  
16891372 A.Huet, and P.Derreumaux (2006).
Impact of the mutation A21G (Flemish variant) on Alzheimer's beta-amyloid dimers by molecular dynamics simulations.
  Biophys J, 91, 3829-3840.  
17173479 A.Trovato, F.Chiti, A.Maritan, and F.Seno (2006).
Insight into the structure of amyloid fibrils from the analysis of globular proteins.
  PLoS Comput Biol, 2, e170.  
16555351 G.T.Dolphin, P.Dumy, and J.Garcia (2006).
Control of amyloid beta-peptide protofibril formation by a designed template assembly.
  Angew Chem Int Ed Engl, 45, 2699-2702.  
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.  
16765899 H.H.Tsai, K.Gunasekaran, and R.Nussinov (2006).
Sequence and structure analysis of parallel beta helices: implication for constructing amyloid structural models.
  Structure, 14, 1059-1072.  
16826550 J.Danielsson, A.Andersson, J.Jarvet, and A.Gräslund (2006).
15N relaxation study of the amyloid beta-peptide: structural propensities and persistence length.
  Magn Reson Chem, 44, S114-S121.  
17047863 J.S.Nowick (2006).
What I have learned by using chemical model systems to study biomolecular structure and interactions.
  Org Biomol Chem, 4, 3869-3885.  
16679374 J.Zheng, B.Ma, C.J.Tsai, and R.Nussinov (2006).
Structural stability and dynamics of an amyloid-forming peptide GNNQQNY from the yeast prion sup-35.
  Biophys J, 91, 824-833.  
17021379 J.Zheng, B.Ma, and R.Nussinov (2006).
Consensus features in amyloid fibrils: sheet-sheet recognition via a (polar or nonpolar) zipper structure.
  Phys Biol, 3, P1-P4.  
17108084 K.Iwata, T.Fujiwara, Y.Matsuki, H.Akutsu, S.Takahashi, H.Naiki, and Y.Goto (2006).
3D structure of amyloid protofilaments of beta2-microglobulin fragment probed by solid-state NMR.
  Proc Natl Acad Sci U S A, 103, 18119-18124.
PDB code: 2e8d
17093048 K.Makabe, D.McElheny, V.Tereshko, A.Hilyard, G.Gawlak, S.Yan, A.Koide, and S.Koide (2006).
Atomic structures of peptide self-assembly mimics.
  Proc Natl Acad Sci U S A, 103, 17753-17758.
PDB codes: 2af5 2fkg 2fkj 2hkd
17060612 N.Ferguson, J.Becker, H.Tidow, S.Tremmel, T.D.Sharpe, G.Krause, J.Flinders, M.Petrovich, J.Berriman, H.Oschkinat, and A.R.Fersht (2006).
General structural motifs of amyloid protofilaments.
  Proc Natl Acad Sci U S A, 103, 16248-16253.
PDB code: 2nnt
16843895 N.Haspel, D.Zanuy, C.Alemán, H.Wolfson, and R.Nussinov (2006).
De novo tubular nanostructure design based on self-assembly of beta-helical protein motifs.
  Structure, 14, 1137-1148.  
16563741 R.Nelson, and D.Eisenberg (2006).
Recent atomic models of amyloid fibril structure.
  Curr Opin Struct Biol, 16, 260-265.  
17122841 R.Riek (2006).
Cell biology: infectious Alzheimer's disease?
  Nature, 444, 429-431.  
16634632 T.Sato, P.Kienlen-Campard, M.Ahmed, W.Liu, H.Li, J.I.Elliott, S.Aimoto, S.N.Constantinescu, J.N.Octave, and S.O.Smith (2006).
Inhibitors of amyloid toxicity based on beta-sheet packing of Abeta40 and Abeta42.
  Biochemistry, 45, 5503-5516.  
16965061 W.Chen, N.Mousseau, and P.Derreumaux (2006).
The conformations of the amyloid-beta (21-30) fragment can be described by three families in solution.
  J Chem Phys, 125, 084911.  
17038501 W.Kim, and M.H.Hecht (2006).
Generic hydrophobic residues are sufficient to promote aggregation of the Alzheimer's Abeta42 peptide.
  Proc Natl Acad Sci U S A, 103, 15824-15829.  
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.  
16533917 W.Guo, J.E.Shea, and R.S.Berry (2005).
The physics of the interactions governing folding and association of proteins.
  Ann N Y Acad Sci, 1066, 34-53.  
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 codes are shown on the right.