Beta Amyloid Fibrils Formation Structure & Growth ~ Top 100 Papers on Amyloid Beta Fibrils Formation Structure & Growth~

Beta Amyloid Fibrils Formation Structure & Growth  ~ Top 100 Papers on Amyloid Beta Fibrils Formation Structure & Growth~ 

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The simulation: fibrils are thought to be symmetric assemblies, which means that they are formed by stacking together many identical copies of a protein or peptide. What you see on your screen are 12 copies of the Abeta(10-40) sequence (our collaborators tell us that residues 1-9 are likely to be disordered and outside the core of the fibril). There will be a low-resolution simulation (no sidechains visible, lots of movement), followed by a high-resolution refinement (sidechains visible in the left panel, simulation appears to go much more slowly). Not all low-resolution trajectories will go on to high-res refinement -- we are filtering for conformations which satisfy the experimental constraints.

1.

Molecular Structures of Quiescently Grown and Brain-Derived Polymorphic Fibrils of the Alzheimer Amyloid Aβ_9-40 Peptide: A Comparison to Agitated Fibrils

Chun Wu, Michael T. Bowers, Joan-Emma Shea

PLoS Comput Biol. 2010 March; 6(3): e1000693. Published online 2010 March 5.doi: 10.1371/journal.pcbi.1000693

PMCID: 

PMC2832665

AbstractFull TextPDF–852KSupplementary Material

2.

αB-Crystallin inhibits the cell toxicity associated with amyloid fibril formation by κ-casein and the amyloid-β peptide

Francis C. Dehle, Heath Ecroyd, Ian F. Musgrave, John A. Carver

Cell Stress Chaperones. 2010 November; 15(6): 1013–1026. Published online 2010 July 15.doi: 10.1007/s12192-010-0212-z

PMCID: 

PMC3024074

AbstractFull TextPDF–795K

3.

BETASCAN: Probable β-amyloids Identified by Pairwise Probabilistic Analysis

Allen W. Bryan, Jr., Matthew Menke, Lenore J. Cowen, Susan L. Lindquist, Bonnie Berger

PLoS Comput Biol. 2009 March; 5(3): e1000333. Published online 2009 March 27.doi: 10.1371/journal.pcbi.1000333

PMCID: 

PMC2653728

AbstractFull TextPDF–978KSupplementary Material

4.

β arcades: recurring motifs in naturally occurring and disease-related amyloid fibrils

Andrey V. Kajava, Ulrich Baxa, Alasdair C. Steven

FASEB J. 2010 May; 24(5): 1311–1319. doi: 10.1096/fj.09-145979

PMCID: 

PMC2879952

AbstractFull Text

5.

Microscopic factors that control β-sheet registry in Amyloid fibrils formed by 11–25 fragment of Amyloid β peptide: Insights from computer simulations

Lacramioara Negureanu, Andrij Baumketner

J Mol Biol. Author manuscript; available in PMC 2010 June 26.

Published in final edited form as: J Mol Biol. 2009 June 26; 389(5): 921–937. Published online 2009 May 3. doi: 10.1016/j.jmb.2009.04.058

PMCID: 

PMC2696565

AbstractFull TextPDF–3.6MSupplementary Material

6.

Molecular Modeling of the Misfolded Insulin Subunit and Amyloid Fibril

Jay H. Choi, Barnaby C.H. May, Holger Wille, Fred E. Cohen

Biophys J. 2009 December 16; 97(12): 3187–3195. doi: 10.1016/j.bpj.2009.09.042

PMCID: 

PMC2793351

AbstractFull TextPDF–724KSupplementary Material

7.

Strategies for Extracting Structural Information from 2D IR Spectroscopy of Amyloid: Application to Islet Amyloid Polypeptide

David B. Strasfeld, Yun L. Ling, Ruchi Gupta, Daniel P. Raleigh, Martin T. Zanni

J Phys Chem B. Author manuscript; available in PMC 2010 July 12.

Published in final edited form as: J Phys Chem B. 2009 November 26; 113(47): 15679–15691.doi: 10.1021/jp9072203

PMCID: 

PMC2901919

AbstractFull TextPDF–4.4MSupplementary Material

8.

A Multiscale Approach to Characterize the Early Aggregation Steps of the Amyloid-Forming Peptide GNNQQNY from the Yeast Prion Sup-35

Jessica Nasica-Labouze, Massimiliano Meli, Philippe Derreumaux, Giorgio Colombo, Normand Mousseau

PLoS Comput Biol. 2011 May; 7(5): e1002051. Published online 2011 May 19.doi: 10.1371/journal.pcbi.1002051

PMCID: 

PMC3098217

AbstractFull TextPDF–999KSupplementary Material

9.

A method for probing the mutational landscape of amyloid structure

Charles W. O'Donnell, Jérôme Waldispühl, Mieszko Lis, Randal Halfmann, Srinivas Devadas, Susan Lindquist, Bonnie Berger

Bioinformatics. 2011 July 1; 27(13): i34–i42. Published online 2011 June 14.doi: 10.1093/bioinformatics/btr238

PMCID: 

PMC3117379

AbstractFull TextSupplementary Material

10.

Replica Exchange Simulations of the Thermodynamics of Aβ Fibril Growth

Takako Takeda, Dmitri K. Klimov

Biophys J. 2009 January 21; 96(2): 442–452. doi: 10.1016/j.bpj.2008.10.008

PMCID: 

PMC2716483

AbstractFull TextPDF–948KSupplementary Material

11.

Computational backbone mutagenesis of Aβ peptides: Probing the role of backbone hydrogen bonds in aggregation

Takako Takeda, Dmitri K. Klimov

J Phys Chem B. Author manuscript; available in PMC 2011 April 15.

Published in final edited form as: J Phys Chem B. 2010 April 15; 114(14): 4755–4762.doi: 10.1021/jp911533q

PMCID: 

PMC2862262

AbstractFull TextPDF–1.5MSupplementary Material

12.

Thermodynamic Selection of Steric Zipper Patterns in the Amyloid Cross-β Spine

Jiyong Park, Byungnam Kahng, Wonmuk Hwang

PLoS Comput Biol. 2009 September; 5(9): e1000492. Published online 2009 September 4.doi: 10.1371/journal.pcbi.1000492

PMCID: 

PMC2723932

AbstractFull TextPDF–1.5MSupplementary Material

13.

The Sulfated Triphenyl Methane Derivative Acid Fuchsin is a Potent Inhibitor of AmyloidFormation by Human Islet Amyloid Polypeptide and Protects Against the Toxic Effects ofAmyloid Formation

Fanling Meng, Andisheh Abedini, Annette Plesner, Chris T Middleton, Kathryn J. Potter, Martin T Zanni, C. Bruce Verchere, Daniel P. Raleigh

J Mol Biol. Author manuscript; available in PMC 2011 July 16.

Published in final edited form as: J Mol Biol. 2010 July 16; 400(3): 555–566. Published online 2010 May 7. doi: 10.1016/j.jmb.2010.05.001

PMCID: 

PMC2902639

AbstractFull TextPDF–4.4MSupplementary Material

14.

Fibril Fragmentation Enhances Amyloid Cytotoxicity

Wei-Feng Xue, Andrew L. Hellewell, Walraj S. Gosal, Steve W. Homans, Eric W. Hewitt, Sheena E. Radford

J Biol Chem. 2009 December 4; 284(49): 34272–34282. Published online 2009 October 6.doi: 10.1074/jbc.M109.049809

PMCID: 

PMC2797196

AbstractFull Text

15.

Atomic-Scale Simulations Confirm that Soluble β-Sheet-Rich Peptide Self-Assemblies Provide Amyloid Mimics Presenting Similar Conformational Properties

Xiang Yu, Jingdai Wang, Jui-Chen Yang, Qiuming Wang, Stephen Z.D. Cheng, Ruth Nussinov, Jie Zheng

Biophys J. 2010 January 6; 98(1): 27–36. doi: 10.1016/j.bpj.2009.10.003

PMCID: 

PMC2800962

AbstractFull TextPDF–1.5MSupplementary Material

16.

Minimalist design of water-soluble cross-β architecture

Matthew Biancalana, Koki Makabe, Shohei Koide

Proc Natl Acad Sci U S A. 2010 February 23; 107(8): 3469–3474. Published online 2010 February 4.doi: 10.1073/pnas.0912654107

PMCID: 

PMC2840449

AbstractFull TextPDF–463KSupplementary Material

17.

Towards a Pharmacophore for Amyloid

Meytal Landau, Michael R. Sawaya, Kym F. Faull, Arthur Laganowsky, Lin Jiang, Stuart A. Sievers, Jie Liu, Jorge R. Barrio, David Eisenberg

PLoS Biol. 2011 June; 9(6): e1001080. Published online 2011 June 14.doi: 10.1371/journal.pbio.1001080

PMCID: 

PMC3114762

AbstractFull TextPDF–1.0MSupplementary Material

18.

Bacterial Inclusion Bodies Contain Amyloid-Like Structure

Lei Wang, Samir K Maji, Michael R Sawaya, David Eisenberg, Roland Riek

PLoS Biol. 2008 August; 6(8): e195. Published online 2008 August 5.doi: 10.1371/journal.pbio.0060195

PMCID: 

PMC2494559

AbstractFull TextPDF–993KSupplementary Material

19.

The Ability of Rodent Islet Amyloid Polypeptide to Inhibit Amyloid Formation by Human Islet Amyloid Polypeptide Has Important Implications For the Mechanism of AmyloidFormation and the Design of Inhibitors.

Ping Cao, Fanling Meng, Andisheh Abedini, Daniel P Raleigh

Biochemistry. Author manuscript; available in PMC 2011 February 9.

Published in final edited form as: Biochemistry. 2010 February 9; 49(5): 872–881.doi: 10.1021/bi901751b

PMCID: 

PMC2882292

AbstractFull TextPDF–1.2MSupplementary Material

20.

Stabilization of neurotoxic Alzheimer amyloid-β oligomers by protein engineering

Anders Sandberg, Leila M. Luheshi, Sofia Söllvander, Teresa Pereira de Barros, Bertil Macao, Tuomas P. J. Knowles, Henrik Biverstål, Christofer Lendel, Frida Ekholm-Petterson, Anatoly Dubnovitsky, Lars Lannfelt, Christopher M. Dobson, Torleif Härd

Proc Natl Acad Sci U S A. 2010 August 31; 107(35): 15595–15600. Published online 2010 August 16.doi: 10.1073/pnas.1001740107

PMCID: 

PMC2932621

AbstractFull TextPDF–633KSupplementary Material

21.

Phospholipids enhance nucleation but not elongation of apolipoprotein C-II amyloid fibrils

Timothy M. Ryan, Chai L. Teoh, Michael D. W. Griffin, Michael F. Bailey, Peter Schuck, Geoffrey J. Howlett

J Mol Biol. Author manuscript; available in PMC 2011 June 25.

Published in final edited form as: J Mol Biol. 2010 June 25; 399(5): 731–740. Published online 2010 April 28. doi: 10.1016/j.jmb.2010.04.042

PMCID: 

PMC2887044

AbstractFull TextPDF–1.6M

22.

Heterologous Stacking of Prion Protein Peptides Reveals Structural Details of Fibrils and Facilitates Complete Inhibition of Fibril Growth

Ronald S. Boshuizen, Veronica Schulz, Michela Morbin, Giulia Mazzoleni, Rob H. Meloen, Johannes P. M. Langedijk

J Biol Chem. 2009 May 8; 284(19): 12809–12820. doi: 10.1074/jbc.M809151200

PMCID: 

PMC2676011

AbstractFull TextSupplementary Material

23.

Side chain interactions can impede amyloid fibril growth: Replica exchange simulations of Aβ peptide mutant

Takako Takeda, Dmitri K. Klimov

J Phys Chem B. Author manuscript; available in PMC 2010 September 3.

Published in final edited form as: J Phys Chem B. 2009 September 3; 113(35): 11848–11857.doi: 10.1021/jp904070w

PMCID: 

PMC2765228

AbstractFull TextPDF–2.0MSupplementary Material

24.

Evidence for Novel β-Sheet Structures in Iowa Mutant β-Amyloid Fibrils

Robert Tycko, Kimberly L. Sciarretta, Joseph P. R. O. Orgel, Stephen C. Meredith

Biochemistry. Author manuscript; available in PMC 2010 July 27.

Published in final edited form as: Biochemistry. 2009 July 7; 48(26): 6072–6084.doi: 10.1021/bi9002666

PMCID: 

PMC2910621

AbstractFull TextPDF–4.4MSupplementary Material

25.

Dissociation from the Oligomeric State Is the Rate-limiting Step in Fibril Formation by κ-Casein

Heath Ecroyd, Tomas Koudelka, David C. Thorn, Danielle M. Williams, Glyn Devlin, Peter Hoffmann, John A. Carver

J Biol Chem. 2008 April 4; 283(14): 9012–9022. doi: 10.1074/jbc.M709928200

PMCID: 

PMC2431022

AbstractFull Text

26.

Residue-Specific, Real-Time Characterization of Lag-Phase Species and Fibril Growth During Amyloid Formation: A Combined Fluorescence and IR Study of p-Cyanophenylalanine Analogs of Islet Amyloid Polypeptide

Peter Marek, Sudipta Mukherjee, Martin T. Zanni, Daniel P. Raleigh

J Mol Biol. Author manuscript; available in PMC 2011 March 21.

Published in final edited form as: J Mol Biol. 2010 July 23; 400(4): 878–888. Published online 2010 June 1. doi: 10.1016/j.jmb.2010.05.041

PMCID: 

PMC3061969

AbstractFull TextPDF–1.5MSupplementary Material

27.

Loss of Metal Ions, Disulfide Reduction and Mutations Related to Familial ALS PromoteFormation of Amyloid-Like Aggregates from Superoxide Dismutase

Zeynep A. Oztug Durer, Jeffrey A. Cohlberg, Phong Dinh, Shelby Padua, Krista Ehrenclou, Sean Downes, James K. Tan, Yoko Nakano, Christopher J. Bowman, Jessica L. Hoskins, Chuhee Kwon, Andrew Z. Mason, Jorge A. Rodriguez, Peter A. Doucette, Bryan F. Shaw, Joan Selverstone Valentine

PLoS ONE. 2009; 4(3): e5004. Published online 2009 March 27. doi: 10.1371/journal.pone.0005004

PMCID: 

PMC2659422

AbstractFull TextPDF–532KSupplementary Material

28.

Molecular basis for insulin fibril assembly

Magdalena I. Ivanova, Stuart A. Sievers, Michael R. Sawaya, Joseph S. Wall, David Eisenberg

Proc Natl Acad Sci U S A. 2009 November 10; 106(45): 18990–18995. Published online 2009 October 28. doi: 10.1073/pnas.0910080106

PMCID: 

PMC2776439

AbstractFull TextPDF–2.5MSupplementary Material

29.

Cytotoxic Aggregation and Amyloid Formation by the Myostatin Precursor Protein

Carlene S. Starck, Andrew J. Sutherland-Smith

PLoS One. 2010; 5(2): e9170. Published online 2010 February 11. doi: 10.1371/journal.pone.0009170

PMCID: 

PMC2820090

AbstractFull TextPDF–4.5MSupplementary Material

30.

Inhibitors of amyloid toxicity based on β-sheet packing of Aβ40 and Aβ42

Takeshi Sato, Pascal Kienlen-Campard, Mahiuddin Ahmed, Wei Liu, Huilin Li, James I. Elliott, Saburo Aimoto, Stefan N. Constantinescu, Jean-Noel Octave, Steven O. Smith

Biochemistry. Author manuscript; available in PMC 2008 December 4.

Published in final edited form as: Biochemistry. 2006 May 2; 45(17): 5503–5516.doi: 10.1021/bi052485f

PMCID: 

PMC2593882

AbstractFull TextPDF–3.3MSupplementary Material

31.

Polymorphism in Alzheimer Aβ Amyloid Organization Reflects Conformational Selection in a Rugged Energy Landscape

Yifat Miller, Buyong Ma, Ruth Nussinov

Chem Rev. 2010 August 11; 110(8): 4820–4838. Published online 2010 April 19.doi: 10.1021/cr900377t

PMCID: 

PMC2920034

Full TextPDF–3.5M

32.

Binding mode of Thioflavin T and other molecular probes in the context of amyloid fibrils—current status

Minna Groenning

J Chem Biol. 2010 March; 3(1): 1–18. Published online 2009 August 20. doi: 10.1007/s12154-009-0027-5

PMCID: 

PMC2816742

AbstractFull TextPDF–754K

33.

Structural basis of infectious and non-infectious amyloids

Ulrich Baxa

Curr Alzheimer Res. Author manuscript; available in PMC 2008 October 22.

Published in final edited form as: Curr Alzheimer Res. 2008 June; 5(3): 308–318.

PMCID: 

PMC2570950

AbstractFull TextPDF–1.7M

34.

Molecular Mechanism of Thioflavin-T Binding to Amyloid Fibrils

Matthew Biancalana, Shohei Koide

Biochim Biophys Acta. Author manuscript; available in PMC 2011 July 1.

Published in final edited form as: Biochim Biophys Acta. 2010 July; 1804(7): 1405–1412. Published online 2010 April 22. doi: 10.1016/j.bbapap.2010.04.001

PMCID: 

PMC2880406

AbstractFull TextPDF–1.4M

35.

What Determines the Structure and Stability of KFFE Monomers, Dimers, and Protofibrils?

Giovanni Bellesia, Joan-Emma Shea

Biophys J. 2009 February 4; 96(3): 875–886. doi: 10.1016/j.bpj.2008.10.040

PMCID: 

PMC2716633

AbstractFull TextPDF–1.1MSupplementary Material

36.

Amyloid Fibril-Like Structure Underlies the Aggregate Structure across the pH Range for β-Lactoglobulin

Mark R.H. Krebs, Glyn L. Devlin, Athene M. Donald

Biophys J. 2009 June 17; 96(12): 5013–5019. doi: 10.1016/j.bpj.2009.03.028

PMCID: 

PMC2712037

AbstractFull TextPDF–411KSupplementary Material

37.

Induced β-Barrel Formation of the Alzheimer's Aβ25–35 Oligomers on Carbon Nanotube Surfaces: Implication for Amyloid Fibril Inhibition

Zhaoming Fu, Yin Luo, Philippe Derreumaux, Guanghong Wei

Biophys J. 2009 September 16; 97(6): 1795–1803. doi: 10.1016/j.bpj.2009.07.014

PMCID: 

PMC2749794

AbstractFull TextPDF–1.9MSupplementary Material

38.

Inhibiting α-Synuclein Oligomerization by Stable Cell-Penetrating β-Synuclein Fragments Recovers Phenotype of Parkinson's Disease Model Flies

Ronit Shaltiel-Karyo, Moran Frenkel-Pinter, Nirit Egoz-Matia, Anat Frydman-Marom, Deborah E. Shalev, Daniel Segal, Ehud Gazit

PLoS One. 2010; 5(11): e13863. Published online 2010 November 10.doi: 10.1371/journal.pone.0013863

PMCID: 

PMC2978097

AbstractFull TextPDF–1.9MSupplementary Material

39.

Insight into the Structure of Amyloid Fibrils from the Analysis of Globular Proteins

Antonio Trovato, Fabrizio Chiti, Amos Maritan, Flavio Seno

PLoS Comput Biol. 2006 December; 2(12): e170. Prepublished online 2006 October 30. Published online 2006 December 15. doi: 10.1371/journal.pcbi.0020170

PMCID: 

PMC1698942

AbstractFull TextPDF–464K

40.

Spatial Extent of Charge Repulsion Regulates Assembly Pathways for Lysozyme AmyloidFibrils

Shannon E. Hill, Tatiana Miti, Tyson Richmond, Martin Muschol

PLoS One. 2011; 6(4): e18171. Published online 2011 April 5. doi: 10.1371/journal.pone.0018171

PMCID: 

PMC3071722

AbstractFull TextPDF–1.4M

41.

Seeded growth of β-amyloid fibrils from Alzheimer's brain-derived fibrils produces a distinct fibril structure

Anant K. Paravastu, Isam Qahwash, Richard D. Leapman, Stephen C. Meredith, Robert Tycko

Proc Natl Acad Sci U S A. 2009 May 5; 106(18): 7443–7448. Published online 2009 April 17.doi: 10.1073/pnas.0812033106

PMCID: 

PMC2678625

AbstractFull TextPDF–1.1MSupplementary Material

42.

Temperature-Induced Dissociation of Aβ Monomers from Amyloid Fibril

Takako Takeda, Dmitri K. Klimov

Biophys J. 2008 August 15; 95(4): 1758–1772. Published online 2008 May 23.doi: 10.1529/biophysj.108.131698

PMCID: 

PMC2483770

AbstractFull TextPDF–1.1M

43.

Structural Elements Regulating Amyloidogenesis: A Cholinesterase Model System

Létitia Jean, Chiu Fan Lee, Michael Shaw, David J. Vaux

PLoS ONE. 2008; 3(3): e1834. Published online 2008 March 19. doi: 10.1371/journal.pone.0001834

PMCID: 

PMC2265548

AbstractFull TextPDF–1.7M

44.

Formation and Growth of Oligomers: A Monte Carlo Study of an Amyloid Tau Fragment

Da-Wei Li, Sandipan Mohanty, Anders Irbäck, Shuanghong Huo

PLoS Comput Biol. 2008 December; 4(12): e1000238. Published online 2008 December 5.doi: 10.1371/journal.pcbi.1000238

PMCID: 

PMC2583953

AbstractFull TextPDF–658KSupplementary Material

45.

The Functional Curli Amyloid Is Not Based on In-register Parallel β-Sheet Structure

Frank Shewmaker, Ryan P. McGlinchey, Kent R. Thurber, Peter McPhie, Fred Dyda, Robert Tycko, Reed B. Wickner

J Biol Chem. 2009 September 11; 284(37): 25065–25076. Published online 2009 July 1.doi: 10.1074/jbc.M109.007054

PMCID: 

PMC2757210

AbstractFull TextSupplementary Material

46.

αB-crystallin, a small heat-shock protein, prevents the amyloid fibril growth of anamyloid β-peptide and β₂-microglobulin

Bakthisaran Raman, Tadato Ban, Miyo Sakai, Saloni Y. Pasta, Tangirala Ramakrishna, Hironobu Naiki, Yuji Goto, Ch. Mohan Rao

Biochem J. 2005 December 15; 392(Pt 3): 573–581. Prepublished online 2005 August 1. Published online 2005 December 6. doi: 10.1042/BJ20050339

PMCID: 

PMC1316297

AbstractFull TextPDF–446K

47.

Structure-based prediction reveals capping motifs that inhibit β-helix aggregation

Allen W. Bryan, Jr., Jennifer L. Starner-Kreinbrink, Raghavendra Hosur, Patricia L. Clark, Bonnie Berger

Proc Natl Acad Sci U S A. 2011 July 5; 108(27): 11099–11104. Published online 2011 June 17.doi: 10.1073/pnas.1017504108

PMCID: 

PMC3131356

AbstractFull TextPDF–1.7MSupplementary Material

48.

The effects of sodium sulfate, glycosaminoglycans, and Congo red on the structure, stability, and amyloid formation of an immunoglobulin light-chain protein

Richard W. Mclaughlin, Janelle K. De Stigter, Laura A. Sikkink, Elizabeth M. Baden, Marina Ramirez-Alvarado

Protein Sci. 2006 July; 15(7): 1710–1722. doi: 10.1110/ps.051997606

PMCID: 

PMC2242560

AbstractFull TextPDF–869K

49.

Paired β-sheet structure of an Aβ(1-40) amyloid fibril revealed by electron microscopy

Carsten Sachse, Marcus Fändrich, Nikolaus Grigorieff

Proc Natl Acad Sci U S A. 2008 May 27; 105(21): 7462–7466. Published online 2008 May 15.doi: 10.1073/pnas.0712290105

PMCID: 

PMC2396686

AbstractFull TextPDF–693K

50.

Fibril fragmentation in amyloid assembly and cytotoxicity: When size matters

Wei-Feng Xue, Andrew L Hellewell, Eric W Hewitt, Sheena E Radford

Prion. 2010 Jan-Mar; 4(1): 20–25.

PMCID: 

PMC2850416

AbstractFull TextPDF–807K

51.

Existence of Different Structural Intermediates on the Fibrillation Pathway of Human Serum Albumin

Josué Juárez, Pablo Taboada, Víctor Mosquera

Biophys J. 2009 March 18; 96(6): 2353–2370. doi: 10.1016/j.bpj.2008.12.3901

PMCID: 

PMC2907680

AbstractFull TextPDF–1.2MSupplementary Material

52.

N-terminal Domains Elicit Formation of Functional Pmel17 Amyloid Fibrils

Brenda Watt, Guillaume van Niel, Douglas M. Fowler, Ilse Hurbain, Kelvin C. Luk, Steven E. Stayrook, Mark A. Lemmon, Graça Raposo, James Shorter, Jeffery W. Kelly, Michael S. Marks

J Biol Chem. 2009 December 18; 284(51): 35543–35555. Published online 2009 October 19.doi: 10.1074/jbc.M109.047449

PMCID: 

PMC2790984

AbstractFull Text

53.

Influence of preformed Asp23-Lys28 salt bridge on the conformational fluctuations of monomers and dimers of Aβ peptides with implications for rates of fibril formation

Govardhan Reddy, John E. Straub, Devarajan Thirumalai

J Phys Chem B. Author manuscript; available in PMC 2011 May 20.

Published in final edited form as: J Phys Chem B. 2009 January 29; 113(4): 1162–1172.doi: 10.1021/jp808914c

PMCID: 

PMC3098509

AbstractFull TextPDF–2.1M

54.

Granular Assembly of α-Synuclein Leading to the Accelerated Amyloid Fibril Formationwith Shear Stress

Ghibom Bhak, Jung-Ho Lee, Ji-Sook Hahn, Seung R. Paik

PLoS ONE. 2009; 4(1): e4177. Published online 2009 January 12. doi: 10.1371/journal.pone.0004177

PMCID: 

PMC2613562

AbstractFull TextPDF–535KSupplementary Material

55.

Plasticity of amyloid fibrils

Ronald Wetzel, Shankaramma Shivaprasad, Angela D. Williams

Biochemistry. Author manuscript; available in PMC 2008 August 27.

Published in final edited form as: Biochemistry. 2007 January 9; 46(1): 1–10. doi: 10.1021/bi0620959

PMCID: 

PMC2526019

AbstractFull TextPDF–1.5M

56.

A critical assessment of the role of helical intermediates in amyloid formation by natively unfolded proteins and polypeptides

Andisheh Abedini, Daniel P. Raleigh

Protein Eng Des Sel. 2009 August; 22(8): 453–459. Published online 2009 July 12.doi: 10.1093/protein/gzp036

PMCID: 

PMC2719502

AbstractFull TextPDF–131K

57.

Dynamics of locking of peptides onto growing amyloid fibrils

Govardhan Reddy, John E. Straub, D. Thirumalai

Proc Natl Acad Sci U S A. 2009 July 21; 106(29): 11948–11953. Published online 2009 July 6.doi: 10.1073/pnas.0902473106

PMCID: 

PMC2715474

AbstractFull TextPDF–1.4MSupplementary Material

58.

A Helical Structural Nucleus Is the Primary Elongating Unit of Insulin Amyloid Fibrils

Bente Vestergaard, Minna Groenning, Manfred Roessle, Jette S Kastrup, Marco van de Weert, James M Flink, Sven Frokjaer, Michael Gajhede, Dmitri I Svergun

PLoS Biol. 2007 May; 5(5): e134. Published online 2007 May 1. doi: 10.1371/journal.pbio.0050134

PMCID: 

PMC1858711

AbstractFull TextPDF–573KSupplementary Material

59.

Probing the mechanisms of fibril formation using lattice models

Mai Suan Li, D. K. Klimov, J. E. Straub, D. Thirumalai

J Chem Phys. 2008 November 7; 129(17): 175101. Published online 2008 November 4.doi: 10.1063/1.2989981

PMCID: 

PMC2671665

AbstractFull TextPDF–911K

60.

Fibrillar Oligomers Nucleate the Oligomerization of Monomeric Amyloid β but Do Not Seed Fibril Formation

Jessica W. Wu, Leonid Breydo, J. Mario Isas, Jerome Lee, Yurii G. Kuznetsov, Ralf Langen, Charles Glabe

J Biol Chem. 2010 February 26; 285(9): 6071–6079. Published online 2009 December 15.doi: 10.1074/jbc.M109.069542

PMCID: 

PMC2825401

AbstractFull TextSupplementary Material

61.

Polymorphic Fibril Formation by Residues 10–40 of the Alzheimer's β-Amyloid Peptide

Anant K. Paravastu, Aneta T. Petkova, Robert Tycko

Biophys J. 2006 June 15; 90(12): 4618–4629. Published online 2006 March 24.doi: 10.1529/biophysj.105.076927

PMCID: 

PMC1471876

AbstractFull TextPDF–279K

62.

The inhibitory effect of pyrroloquinoline quinone on the amyloid formation and cytotoxicity of truncated alpha-synuclein

Jihoon Kim, Ryuichi Harada, Masaki Kobayashi, Natsuki Kobayashi, Koji Sode

Mol Neurodegener. 2010; 5: 20. Published online 2010 May 20. doi: 10.1186/1750-1326-5-20

PMCID: 

PMC2881056

AbstractFull TextPDF–1.3M

63.

Heparin Induces Harmless Fibril Formation in Amyloidogenic W7FW14F Apomyoglobin and Amyloid Aggregation in Wild-Type Protein In Vitro

Silvia Vilasi, Rosalba Sarcina, Rosa Maritato, Antonella De Simone, Gaetano Irace, Ivana Sirangelo

PLoS One. 2011; 6(7): e22076. Published online 2011 July 13. doi: 10.1371/journal.pone.0022076

PMCID: 

PMC3135624

AbstractFull TextPDF–1005K

64.

A simple algorithm locates β-strands in the amyloid fibril core of α-synuclein, Aβ, and tau using the amino acid sequence alone

Shahin Zibaee, O. Sumner Makin, Michel Goedert, Louise C. Serpell

Protein Sci. 2007 May; 16(5): 906–918. doi: 10.1110/ps.062624507

Correction in: 

Protein Sci. 2007 June; 16(6): 1242.

PMCID: 

PMC2206631

AbstractFull TextPDF–513KCorrection

65.

Structural conversion of neurotoxic amyloid-β(1–42) oligomers to fibrils

Mahiuddin Ahmed, Judianne Davis, Darryl Aucoin, Takeshi Sato, Shivani Ahuja, Saburo Aimoto, James I. Elliott, William E. Van Nostrand, Steven O. Smith

Nat Struct Mol Biol. Author manuscript; available in PMC 2010 November 1.

Published in final edited form as: Nat Struct Mol Biol. 2010 May; 17(5): 561–567. Published online 2010 April 11. doi: 10.1038/nsmb.1799

PMCID: 

PMC2922021

AbstractFull TextPDF–962KSupplementary Material

66.

Simulation study on the disordered state of an Alzheimer's β amyloid peptide Aβ(12–36) in water consisting of random-structural, β-structural, and helical clusters

Jinzen Ikebe, Narutoshi Kamiya, Jun-Ichi Ito, Heisaburo Shindo, Junichi Higo

Protein Sci. 2007 August; 16(8): 1596–1608. doi: 10.1110/ps.062721907

PMCID: 

PMC2203368

AbstractFull TextPDF–915K

67.

Determining the Critical Nucleus and Mechanism of Fibril Elongation of the Alzheimer's Aβ₁₋40 Peptide

Nicolas Lux Fawzi, Yuka Okabe, Eng-Hui Yap, Teresa Head-Gordon

J Mol Biol. Author manuscript; available in PMC 2009 April 27.

Published in final edited form as: J Mol Biol. 2007 January 12; 365(2): 535–550. Published online 2006 October 7. doi: 10.1016/j.jmb.2006.10.011

PMCID: 

PMC2674024

AbstractFull TextPDF–2.2M

68.

Amyloidogenic Potential of Transthyretin Variants: INSIGHTS FROM STRUCTURAL AND COMPUTATIONAL ANALYSES

Laura Cendron, Antonio Trovato, Flavio Seno, Claudia Folli, Beatrice Alfieri, Giuseppe Zanotti, Rodolfo Berni

J Biol Chem. 2009 September 18; 284(38): 25832–25841. Published online 2009 July 14.doi: 10.1074/jbc.M109.017657

PMCID: 

PMC2757985

AbstractFull Text

69.

Amyloidogenesis of Natively Unfolded Proteins

Vladimir N. Uversky

Curr Alzheimer Res. Author manuscript; available in PMC 2009 August 3.

Published in final edited form as: Curr Alzheimer Res. 2008 June; 5(3): 260–287.

PMCID: 

PMC2719783

AbstractFull TextPDF–888K

70.

Methionine oxidation induces amyloid fibril formation by full-length apolipoprotein A-I

Yuan Qi Wong, Katrina J. Binger, Geoffrey J. Howlett, Michael D. W. Griffin

Proc Natl Acad Sci U S A. 2010 February 2; 107(5): 1977–1982. Published online 2010 January 19.doi: 10.1073/pnas.0910136107

PMCID: 

PMC2836622

AbstractFull TextPDF–811KSupplementary Material

71.

Polymorphic Structures of Alzheimer's β-Amyloid Globulomers

Xiang Yu, Jie Zheng

PLoS One. 2011; 6(6): e20575. Published online 2011 June 7. doi: 10.1371/journal.pone.0020575

PMCID: 

PMC3110195

AbstractFull TextPDF–2.9M

72.

Macrocyclic β-Sheet Peptides That Inhibit the Aggregation of a Tau-Protein-Derived Hexapeptide

Jing Zheng, Cong Liu, Michael R. Sawaya, Balraju Vadla, Shafiullah Khan, R. Jeremy Woods, David Eisenberg, Warren J. Goux, James S. Nowick

J Am Chem Soc. 2011 March 9; 133(9): 3144–3157. Published online 2011 February 14.doi: 10.1021/ja110545h

PMCID: 

PMC3048834

AbstractFull TextPDF–6.6MSupplementary Material

73.

Stabilization of a β-hairpin in monomeric Alzheimer's amyloid-β peptide inhibits amyloidformation

Wolfgang Hoyer, Caroline Grönwall, Andreas Jonsson, Stefan Ståhl, Torleif Härd

Proc Natl Acad Sci U S A. 2008 April 1; 105(13): 5099–5104. Published online 2008 March 28.doi: 10.1073/pnas.0711731105

PMCID: 

PMC2278213

AbstractFull TextPDF–1.4M

74.

A Role for Amyloid in Cell Aggregation and Biofilm Formation

Melissa C. Garcia, Janis T. Lee, Caleen B. Ramsook, David Alsteens, Yves F. Dufrêne, Peter N. Lipke

PLoS One. 2011; 6(3): e17632. Published online 2011 March 8. doi: 10.1371/journal.pone.0017632

PMCID: 

PMC3050909

AbstractFull TextPDF–4.1MSupplementary Material

75.

Molecular Dynamics Simulations of Anti-Aggregation Effect of Ibuprofen

Wenling E. Chang, Takako Takeda, E. Prabhu Raman, Dmitri K. Klimov

Biophys J. 2010 June 2; 98(11): 2662–2670. doi: 10.1016/j.bpj.2010.02.031

Correction in: 

Biophys J. 2010 September 8; 99(5): 1684.

PMCID: 

PMC2877328

AbstractFull TextPDF–644KSupplementary MaterialCorrection

76.

Novel Transthyretin Amyloid Fibril Formation Inhibitors: Synthesis, Biological Evaluation, and X-Ray Structural Analysis

Satheesh K. Palaninathan, Nilofar N. Mohamedmohaideen, Elisabetta Orlandini, Gabriella Ortore, Susanna Nencetti, Annalina Lapucci, Armando Rossello, Joel S. Freundlich, James C. Sacchettini

PLoS One. 2009; 4(7): e6290. Published online 2009 July 21. doi: 10.1371/journal.pone.0006290

PMCID: 

PMC2709434

AbstractFull TextPDF–796KSupplementary Material

77.

Structural and Functional Properties of Peptides Based on the N-terminus of HIV-1 gp41 and the C-terminus of the Amyloid-Beta Protein

Larry M. Gordon, Alex Nisthal, Andy B. Lee, Sepehr Eskandari, Piotr Ruchala, Chun-Ling Jung, Alan J. Waring, Patrick W. Mobley

Biochim Biophys Acta. Author manuscript; available in PMC 2009 October 1.

Published in final edited form as: Biochim Biophys Acta. 2008 October; 1778(10): 2127–2137.Published online 2008 May 11. doi: 10.1016/j.bbamem.2008.05.002

PMCID: 

PMC2630332

AbstractFull TextPDF–1.5M

78.

Association Thermodynamics and Conformational Stability of β-Sheet Amyloid β(17-42) Oligomers: Effects of E22Q (Dutch) Mutation and Charge Neutralization

Nikolay Blinov, Lyudmyla Dorosh, David Wishart, Andriy Kovalenko

Biophys J. 2010 January 20; 98(2): 282–296. doi: 10.1016/j.bpj.2009.09.062

PMCID: 

PMC2808487

AbstractFull TextPDF–1.2MSupplementary Material

79.

Probing Energetics of Aβ Fibril Elongation by Molecular Dynamics Simulations

Takako Takeda, Dmitri K. Klimov

Biophys J. 2009 June 3; 96(11): 4428–4437. doi: 10.1016/j.bpj.2009.03.015

PMCID: 

PMC2711452

AbstractFull TextPDF–1.4MSupplementary Material

80.

A MODEL OF AMYLOID’S ROLE IN DISEASE BASED ON FIBRIL FRACTURE

Damien Hall, Herman Edskes

Biophys Chem. Author manuscript; available in PMC 2010 November 1.

Published in final edited form as: Biophys Chem. 2009 November; 145(1): 17–28. Published online 2009 August 18. doi: 10.1016/j.bpc.2009.08.004

PMCID: 

PMC2762754

AbstractFull TextPDF–4.7M

81.

Atomic structure of the cross-β spine of islet amyloid polypeptide (amylin)

Jed J.W. Wiltzius, Stuart A. Sievers, Michael R. Sawaya, Duilio Cascio, Dmitriy Popov, Christian Riekel, David Eisenberg

Protein Sci. 2008 September; 17(9): 1467–1474. doi: 10.1110/ps.036509.108

PMCID: 

PMC2525530

AbstractFull TextPDF–575K

82.

Folding versus aggregation: Polypeptide conformations on competing pathways

Thomas R. Jahn, Sheena E. Radford

Arch Biochem Biophys. 2008 January 1; 469(1): 100–117. doi: 10.1016/j.abb.2007.05.015

PMCID: 

PMC2706318

AbstractFull TextPDF–901K

83.

Amyloidogenic sequences in native protein structures

Susan Tzotzos, Andrew J Doig

Protein Sci. 2010 February; 19(2): 327–348. Published online 2009 December 21. doi: 10.1002/pro.314

PMCID: 

PMC2865711

AbstractFull TextPDF–396K

84.

Denaturation and solvent effect on the conformation and fibril formation of TGFBIp

Heather L. Grothe, Morgan R. Little, Angela S. Cho, Andrew J.W. Huang, Ching Yuan

Mol Vis. 2009; 15: 2617–2626. Published online 2009 December 8.

PMCID: 

PMC2790481

AbstractFull TextPDF–745K

85.

A Common β-Sheet Architecture Underlies in Vitro and in Vivo β₂-Microglobulin AmyloidFibrils

Thomas R. Jahn, Glenys A. Tennent, Sheena E. Radford

J Biol Chem. 2008 June 20; 283(25): 17279–17286. doi: 10.1074/jbc.M710351200

PMCID: 

PMC2427364

AbstractFull TextSupplementary Material

86.

Detecting hidden sequence propensity for amyloid fibril formation

Sukjoon Yoon, William J. Welsh

Protein Sci. 2004 August; 13(8): 2149–2160. doi: 10.1110/ps.04790604

PMCID: 

PMC2279810

AbstractFull TextPDF–328K

87.

The culprit behind amyloid beta peptide related neurotoxicity in Alzheimer's disease: oligomer size or conformation?

Kerensa Broersen, Frederic Rousseau, Joost Schymkowitz

Alzheimers Res Ther. 2010; 2: 12. Published online 2010 July 14. doi: 10.1186/alzrt36

PMCID: 

PMC2949586

AbstractFull TextPDF–400K

88.

Stacked Sets of Parallel, In-register β-Strands of β₂-Microglobulin in Amyloid Fibrils Revealed by Site-directed Spin Labeling and Chemical Labeling

Carol L. Ladner, Min Chen, David P. Smith, Geoffrey W. Platt, Sheena E. Radford, Ralf Langen

J Biol Chem. 2010 May 28; 285(22): 17137–17147. Published online 2010 March 24.doi: 10.1074/jbc.M110.117234

PMCID: 

PMC2878032

AbstractFull Text

89.

Amyloid in the islets of Langerhans: Thoughts and some historical aspects

Per Westermark

Ups J Med Sci. 2011 May; 116(2): 81–89. Published online 2011 April 12.doi: 10.3109/03009734.2011.573884

PMCID: 

PMC3078536

AbstractFull TextPDF–785K

90.

Pyrroloquinoline quinone inhibits the fibrillation of amyloid proteins

Jihoon Kim, Masaki Kobayashi, Makoto Fukuda, Daisuke Ogasawara, Natsuki Kobayashi, Sungwoong Han, Chikashi Nakamura, Masaki Inada, Chisato Miyaura, Kazunori Ikebukuro, Koji Sode

Prion. 2010 Jan-Mar; 4(1): 26–31.

PMCID: 

PMC2850417

AbstractFull TextPDF–939K

91.

Amyloidogenesis Abolished by Proline Substitutions but Enhanced by Lipid Binding

Ping Jiang, Weixin Xu, Yuguang Mu

PLoS Comput Biol. 2009 April; 5(4): e1000357. Published online 2009 April 10.doi: 10.1371/journal.pcbi.1000357

PMCID: 

PMC2663790

AbstractFull TextPDF–1.5MSupplementary Material

92.

Signaling Effect of Amyloid-β₄₂ on the Processing of AβPP

Massimo Tabaton, Xiongwei Zhu, George Perry, Mark A. Smith, Luca Giliberto

Exp Neurol. Author manuscript; available in PMC 2011 January 1.

Published in final edited form as: Exp Neurol. 2010 January; 221(1): 18–25. Published online 2009 September 9. doi: 10.1016/j.expneurol.2009.09.002

PMCID: 

PMC2812589

AbstractFull TextPDF–703K

93.

Early Stages of Amyloid Fibril Formation Studied by Liquid-State NMR: The Peptide Hormone Glucagon

Anna Sigrid Pii Svane, Kasper Jahn, Taru Deva, Anders Malmendal, Daniel Erik Otzen, Jens Dittmer, Niels Chr. Nielsen

Biophys J. 2008 July 1; 95(1): 366–377. Published online 2008 March 13.doi: 10.1529/biophysj.107.122895

PMCID: 

PMC2426625

AbstractFull TextPDF–707K

94.

Lipocalin-type prostaglandin D synthase/β-trace is a major amyloid β-chaperone in human cerebrospinal fluid

Takahisa Kanekiyo, Tadato Ban, Kosuke Aritake, Zhi-Li Huang, Wei-Min Qu, Issay Okazaki, Ikuko Mohri, Shigeo Murayama, Keiichi Ozono, Masako Taniike, Yuji Goto, Yoshihiro Urade

Proc Natl Acad Sci U S A. 2007 April 10; 104(15): 6412–6417. Published online 2007 April 2.doi: 10.1073/pnas.0701585104

PMCID: 

PMC1851035

AbstractFull TextPDF–2.1MSupplementary Material

95.

Two-dimensional IR spectroscopy and isotope labeling defines the pathway of amyloidformation with residue-specific resolution

Sang-Hee Shim, Ruchi Gupta, Yun L. Ling, David B. Strasfeld, Daniel P. Raleigh, Martin T. Zanni

Proc Natl Acad Sci U S A. 2009 April 21; 106(16): 6614–6619. Published online 2009 April 3.doi: 10.1073/pnas.0805957106

PMCID: 

PMC2672516

AbstractFull TextPDF–754KSupplementary Material

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Molecular Dynamics Simulations on the Oligomer-Formation Process of the GNNQQNY Peptide from Yeast Prion Protein Sup35

Zhuqing Zhang, Hao Chen, Hongjun Bai, Luhua Lai

Biophys J. 2007 September 1; 93(5): 1484–1492. Published online 2007 May 4.doi: 10.1529/biophysj.106.100537

PMCID: 

PMC1948036

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Dry amyloid fibril assembly in a yeast prion peptide is mediated by long-lived structures containing water wires

Govardhan Reddy, John E. Straub, D. Thirumalai

Proc Natl Acad Sci U S A. 2010 December 14; 107(50): 21459–21464. Published online 2010 November 22. doi: 10.1073/pnas.1008616107

PMCID: 

PMC3003024

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Peptide Conformation and Supramolecular Organization in Amylin Fibrils: Constraints from Solid State NMR

Sorin Luca, Wai-Ming Yau, Richard Leapman, Robert Tycko

Biochemistry. Author manuscript; available in PMC 2008 October 7.

Published in final edited form as: Biochemistry. 2007 November 27; 46(47): 13505–13522. Published online 2007 November 3. doi: 10.1021/bi701427q

PMCID: 

PMC2562526

AbstractFull TextPDF–5.1MSupplementary Material

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Potentially amyloidogenic conformational intermediates populate the unfolding landscape of transthyretin: Insights from molecular dynamics simulations

J Rui Rodrigues, Carlos J V Simões, Cândida G Silva, Rui M M Brito

Protein Sci. 2010 February; 19(2): 202–219. Published online 2009 November 20. doi: 10.1002/pro.289

PMCID: 

PMC2865717

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Fibril Growth Kinetics Reveal a Region of β₂-microglobulin Important for Nucleation and Elongation of Aggregation

Geoffrey W. Platt, Katy E. Routledge, Steve W. Homans, Sheena E. Radford

J Mol Biol. 2008 April 18; 378(1): 251–263. doi: 10.1016/j.jmb.2008.01.092

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PMC2627305

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Zhang C, Browne A, Kim DY, Tanzi RE. Familial Alzheimer's Disease Mutations in Presenilin 1 Do Not Alter Levels of the Secreted Amyloid-beta Protein Precursor Generated by beta-Secretase Cleavage. Curr Alzheimer Res. 2009 Dec 1; PubMed Abstract

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Lomoio S, Scherini E, Necchi D. Beta-amyloid overload does not directly correlate with SAPK/JNK activation and tau protein phosphorylation in the cerebellar cortex of Ts65Dn mice. Brain Res. 2009 Nov 10;1297:198-206. PubMed Abstract

Levine H, Ding Q, Walker JA, Voss RS, Augelli-Szafran CE. Clioquinol and other hydroxyquinoline derivatives inhibit Abeta(1-42) oligomer assembly. Neurosci Lett. 2009 Nov 6;465(1):99-103. PubMed Abstract

Li M, Inaba M, Guo K, Abraham NG, Ikehara S. Amelioration of cognitive ability in senescence-accelerated mouse prone 8 (SAMP8) by intra-bone marrow-bone marrow transplantation. Neurosci Lett. 2009 Nov 6;465(1):36-40. PubMed Abstract

Harris B, Pereira I, Parkin E. Targeting ADAM10 to lipid rafts in neuroblastoma SH-SY5Y cells impairs amyloidogenic processing of the amyloid precursor protein. Brain Res. 2009 Nov 3;1296:203-15. PubMed Abstract

Juusela P, Tanskanen M, Nieminen A, Uitto VJ, Blåfield H, Kiuru-Enari S. Hereditary gelsolin amyloidosis mimicking Sjögren's syndrome. Clin Rheumatol. 2009 Nov;28(11):1351-4. PubMed Abstract

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Edison P, Brooks DJ, Turkheimer FE, Archer HA, Hinz R. Strategies for the generation of parametric images of [11C]PIB with plasma input functions considering discriminations and reproducibility. Neuroimage. 2009 Nov 1;48(2):329-38. PubMed Abstract

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Mouton PR, Chachich ME, Quigley C, Spangler E, Ingram DK. Caloric restriction attenuates amyloid deposition in middle-aged dtg APP/PS1 mice. Neurosci Lett. 2009 Oct 30;464(3):184-7. PubMed Abstract

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