Literature DB >> 19164927

Computational simulations of the early steps of protein aggregation.

Guanghong Wei1, Normand Mousseau, Philippe Derreumaux.   

Abstract

There is strong evidence that the oligomers of key proteins, formed during the early steps of aggregation, could be the primary toxic species associated with human neuro-degenerative diseases, such as Alzheimer's and prion diseases. Here, we review recent progress in the development of computational approaches in order to understand the structures, dynamics and free energy surfaces of oligomers. We also discuss possible research directions for the coming years.

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Year:  2007        PMID: 19164927      PMCID: PMC2633700          DOI: 10.4161/pri.1.1.3969

Source DB:  PubMed          Journal:  Prion        ISSN: 1933-6896            Impact factor:   3.931


  86 in total

1.  Structural studies of soluble oligomers of the Alzheimer beta-amyloid peptide.

Authors:  T H Huang; D S Yang; N P Plaskos; S Go; C M Yip; P E Fraser; A Chakrabartty
Journal:  J Mol Biol       Date:  2000-03-17       Impact factor: 5.469

Review 2.  Protein folding and misfolding.

Authors:  Christopher M Dobson
Journal:  Nature       Date:  2003-12-18       Impact factor: 49.962

3.  Molecular dynamics simulations of spontaneous fibril formation by random-coil peptides.

Authors:  Hung D Nguyen; Carol K Hall
Journal:  Proc Natl Acad Sci U S A       Date:  2004-11-08       Impact factor: 11.205

4.  Exploring the early steps of amyloid peptide aggregation by computers.

Authors:  Normand Mousseau; Philippe Derreumaux
Journal:  Acc Chem Res       Date:  2005-11       Impact factor: 22.384

5.  Experimental evidence for the reorganization of beta-strands within aggregates of the Abeta(16-22) peptide.

Authors:  Sarah A Petty; Sean M Decatur
Journal:  J Am Chem Soc       Date:  2005-10-05       Impact factor: 15.419

6.  Probing the initial stage of aggregation of the Abeta(10-35)-protein: assessing the propensity for peptide dimerization.

Authors:  Bogdan Tarus; John E Straub; D Thirumalai
Journal:  J Mol Biol       Date:  2004-12-19       Impact factor: 5.469

7.  Coarse-grained protein molecular dynamics simulations.

Authors:  Philippe Derreumaux; Normand Mousseau
Journal:  J Chem Phys       Date:  2007-01-14       Impact factor: 3.488

8.  High-resolution atomic force microscopy of soluble Abeta42 oligomers.

Authors:  Iris A Mastrangelo; Mahiuddin Ahmed; Takeshi Sato; Wei Liu; Chengpu Wang; Paul Hough; Steven O Smith
Journal:  J Mol Biol       Date:  2006-01-30       Impact factor: 5.469

9.  Common core structure of amyloid fibrils by synchrotron X-ray diffraction.

Authors:  M Sunde; L C Serpell; M Bartlam; P E Fraser; M B Pepys; C C Blake
Journal:  J Mol Biol       Date:  1997-10-31       Impact factor: 5.469

10.  Synthetic mammalian prions.

Authors:  Giuseppe Legname; Ilia V Baskakov; Hoang-Oanh B Nguyen; Detlev Riesner; Fred E Cohen; Stephen J DeArmond; Stanley B Prusiner
Journal:  Science       Date:  2004-07-30       Impact factor: 47.728

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  22 in total

Review 1.  Flexibility and binding affinity in protein-ligand, protein-protein and multi-component protein interactions: limitations of current computational approaches.

Authors:  Pierre Tuffery; Philippe Derreumaux
Journal:  J R Soc Interface       Date:  2011-10-12       Impact factor: 4.118

2.  Association thermodynamics and conformational stability of beta-sheet amyloid beta(17-42) oligomers: effects of E22Q (Dutch) mutation and charge neutralization.

Authors:  Nikolay Blinov; Lyudmyla Dorosh; David Wishart; Andriy Kovalenko
Journal:  Biophys J       Date:  2010-01-20       Impact factor: 4.033

3.  Carbon nanotube inhibits the formation of β-sheet-rich oligomers of the Alzheimer's amyloid-β(16-22) peptide.

Authors:  Huiyu Li; Yin Luo; Philippe Derreumaux; Guanghong Wei
Journal:  Biophys J       Date:  2011-11-01       Impact factor: 4.033

4.  Hydration effects on the HET-s prion and amyloid-beta fibrillous aggregates, studied with three-dimensional molecular theory of solvation.

Authors:  Takeshi Yamazaki; Nikolay Blinov; David Wishart; Andriy Kovalenko
Journal:  Biophys J       Date:  2008-08-08       Impact factor: 4.033

5.  Side-chain hydrophobicity and the stability of Aβ₁₆₋₂₂ aggregates.

Authors:  Workalemahu M Berhanu; Ulrich H E Hansmann
Journal:  Protein Sci       Date:  2012-12       Impact factor: 6.725

6.  Direct observations of shifts in the β-sheet register of a protein-peptide complex using explicit solvent simulations.

Authors:  Maria T Panteva; Reza Salari; Monica Bhattacharjee; Lillian T Chong
Journal:  Biophys J       Date:  2011-05-04       Impact factor: 4.033

Review 7.  Amyloid β Protein and Alzheimer's Disease: When Computer Simulations Complement Experimental Studies.

Authors:  Jessica Nasica-Labouze; Phuong H Nguyen; Fabio Sterpone; Olivia Berthoumieu; Nicolae-Viorel Buchete; Sébastien Coté; Alfonso De Simone; Andrew J Doig; Peter Faller; Angel Garcia; Alessandro Laio; Mai Suan Li; Simone Melchionna; Normand Mousseau; Yuguang Mu; Anant Paravastu; Samuela Pasquali; David J Rosenman; Birgit Strodel; Bogdan Tarus; John H Viles; Tong Zhang; Chunyu Wang; Philippe Derreumaux
Journal:  Chem Rev       Date:  2015-03-19       Impact factor: 60.622

8.  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.

Authors:  Naoyuki Miyashita; John E Straub; D Thirumalai
Journal:  J Am Chem Soc       Date:  2009-12-16       Impact factor: 15.419

Review 9.  High-resolution probing of early events in amyloid-β aggregation related to Alzheimer's disease.

Authors:  Bikash R Sahoo; Sarah J Cox; Ayyalusamy Ramamoorthy
Journal:  Chem Commun (Camb)       Date:  2020-04-17       Impact factor: 6.222

10.  Structure and aggregation mechanism of beta(2)-microglobulin (83-99) peptides studied by molecular dynamics simulations.

Authors:  Chungwen Liang; Philippe Derreumaux; Guanghong Wei
Journal:  Biophys J       Date:  2007-08-10       Impact factor: 4.033

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