Coarse-grained and All-atom Simulations towards the Early and Late Steps of Amyloid Fibril Formation

被引：19
作者：
Chiricotto, Mara [1 ]
Thanh Thuy Tran [1 ]
Nguyen, Phuong H. [1 ]
Melchionna, Simone [2 ]
Sterpone, Fabio [1 ]
Derreumaux, Philippe [1 ]
机构：
[1] Univ Paris Diderot, UPR CNRS 9080, Lab Biochim Theor, Sorbonne Paris Cite,IBPC, 13 Rue Pierre & Marie Curie, F-75005 Paris, France
[2] CNR, Ist Sistemi Complessi, Ple A Moro 2, I-00185 Rome, Italy
来源：
ISRAEL JOURNAL OF CHEMISTRY | 2017年 / 57卷 / 7-8期
基金：
欧洲研究理事会;
关键词：
Alzheimer's disease; amyloid simulations; computational chemistry; mutations; oligomerization; BETA-PROTEIN OLIGOMERIZATION; PROTECTIVE A2T MUTATION; OPEP FORCE-FIELD; ALZHEIMERS-DISEASE; A-BETA(16-22) PEPTIDE; PRIMARY NUCLEATION; A-BETA-1-40; DIMER; ENERGY LANDSCAPE; AGGREGATION; DYNAMICS;
D O I：
10.1002/ijch.201600048
中图分类号：
O6 [化学];
学科分类号：
0703 ;
摘要：
Alzheimer's disease is the most common neurodegenerative disease. Experiments and computer simulations can complement one another to provide a full and in-depth understanding of many aspects in the amyloid field at the atomistic level. Here, we review results of our coarse-grained and all-atom simulations in aqueous solution aimed at determining: 1) early aggregation steps of short linear peptides; 2) nucleation size number; 3) solution structure of the A beta(1-40)/A beta(1-42) wild-type dimers; 4) impact of FAD (familial forms of Alzheimer's disease) mutations on the structure of A beta(1-40)/A beta(1-42) dimers; and 5) impact of protective mutations on the structure of A beta(1-40)/A beta(1-42) dimers.
引用
收藏
页码：564 / 573
页数：10
相关论文
共 121 条
[1]   A Simple Lattice Model That Captures Protein Folding, Aggregation and Amyloid Formation [J].
Abeln, Sanne ;
Vendruscolo, Michele ;
Dobson, Christopher M. ;
Frenkel, Daan .
PLOS ONE, 2014, 9 (01)
[2]   Nucleation Process of a Fibril Precursor in the C-Terminal Segment of Amyloid-β [J].
Baftizadeh, Fahimeh ;
Pietrucci, Fabio ;
Biarnes, Xevi ;
Laio, Alessandro .
PHYSICAL REVIEW LETTERS, 2013, 110 (16)
[3]   Multidimensional View of Amyloid Fibril Nucleation in Atomistic Detail [J].
Baftizadeh, Fahimeh ;
Biarnes, Xevi ;
Pietrucci, Fabio ;
Affinito, Fabio ;
Laio, Alessandro .
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 2012, 134 (08) :3886-3894
[4]   Assessing the Quality of the OPEP Coarse-Grained Force Field [J].
Barducci, Alessandro ;
Bonomi, Massimiliano ;
Derreumaux, Philippe .
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2011, 7 (06) :1928-1934
[5]   Dimer Formation Enhances Structural Differences between Amyloid β-Protein (1-40) and (1-42): An Explicit-Solvent Molecular Dynamics Study [J].
Barz, Bogdan ;
Urbanc, Brigita .
PLOS ONE, 2012, 7 (04)
[6]   Effect of β-sheet propensity on peptide aggregation [J].
Bellesia, Giovanni ;
Shea, Joan-Emma .
JOURNAL OF CHEMICAL PHYSICS, 2009, 130 (14)
[7]   The Alzheimer Disease Protective Mutation A2T Modulates Kinetic and Thermodynamic Properties of Amyloid-β (Aβ) Aggregation [J].
Benilova, Iryna ;
Gallardo, Rodrigo ;
Ungureanu, Andreea-Alexandra ;
Cano, Virginia Castillo ;
Snellinx, An ;
Ramakers, Meine ;
Bartic, Carmen ;
Rousseau, Frederic ;
Schymkowitz, Joost ;
De Strooper, Bart .
JOURNAL OF BIOLOGICAL CHEMISTRY, 2014, 289 (45) :30977-30989
[8]   MUPHY: A parallel MUlti PHYsics/scale code for high performance bio-fluidic simulations [J].
Bernaschi, M. ;
Melchionna, S. ;
Succi, S. ;
Fyta, M. ;
Kaxiras, E. ;
Sircar, J. K. .
COMPUTER PHYSICS COMMUNICATIONS, 2009, 180 (09) :1495-1502
[9]  
Bernstein SL, 2009, NAT CHEM, V1, P326, DOI [10.1038/NCHEM.247, 10.1038/nchem.247]
[10]   Combined Experimental and Simulation Studies Suggest a Revised Mode of Action of the Anti-Alzheimer Disease Drug NQ-Trp [J].
Berthoumieu, Olivia ;
Nguyen, Phuong H. ;
del Castillo-Frias, Maria P. ;
Ferre, Sabrina ;
Tarus, Bogdan ;
Nasica-Labouze, Jessica ;
Noel, Sabrina ;
Saurel, Olivier ;
Rampon, Claire ;
Doig, Andrew J. ;
Derreumaux, Philippe ;
Faller, Peter .
CHEMISTRY-A EUROPEAN JOURNAL, 2015, 21 (36) :12657-12666
12345678910