Low molecular weight oligomers of amyloid peptides display beta-barrel conformations: a replica exchange molecular dynamics study in explicit solvent (Q30156880)

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English	Low molecular weight oligomers of amyloid peptides display beta-barrel conformations: a replica exchange molecular dynamics study in explicit solvent	scientific article

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scholarly article

1 reference

Europe PubMed Central

8 June 2017

Low molecular weight oligomers of amyloid peptides display beta-barrel conformations: a replica exchange molecular dynamics study in explicit solvent (English)

1 reference

Europe PubMed Central

8 June 2017

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molecular dynamics simulation

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author name string

Alfonso De Simone

1

1 reference

Europe PubMed Central

8 June 2017

Philippe Derreumaux

2

1 reference

Europe PubMed Central

8 June 2017

language of work or name

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publication date

1 April 2010

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Europe PubMed Central

8 June 2017

Journal of Chemical Physics

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Europe PubMed Central

8 June 2017

132

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Europe PubMed Central

8 June 2017

165103

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Europe PubMed Central

8 June 2017

16

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Europe PubMed Central

8 June 2017

Protein misfolding, functional amyloid, and human disease

1 reference

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Amyloid beta-protein assembly as a therapeutic target of Alzheimer's disease

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The alternative conformations of amyloidogenic proteins and their multi-step assembly pathways

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Inherent toxicity of aggregates implies a common mechanism for protein misfolding diseases

1 reference

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Structural classification of toxic amyloid oligomers

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Visualization and classification of amyloid beta supramolecular assemblies.

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Cryo-electron microscopy structure of an SH3 amyloid fibril and model of the molecular packing

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Structure of the cross-beta spine of amyloid-like fibrils

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Amyloid beta -protein (Abeta) assembly: Abeta 40 and Abeta 42 oligomerize through distinct pathways

1 reference

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Disordered flanks prevent peptide aggregation

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The role of side-chain interactions in the early steps of aggregation: Molecular dynamics simulations of an amyloid-forming peptide from the yeast prion Sup35

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Energy landscape of amyloidogenic peptide oligomerization by parallel-tempering molecular dynamics simulation: significant role of Asn ladder

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Discrete molecular dynamics simulations of peptide aggregation.

1 reference

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Structures and thermodynamics of Alzheimer's amyloid-beta Abeta(16-35) monomer and dimer by replica exchange molecular dynamics simulations: implication for full-length Abeta fibrillation.

1 reference

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Formation and growth of oligomers: a Monte Carlo study of an amyloid tau fragment

1 reference

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A coarse-grained protein force field for folding and structure prediction.

1 reference

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PEP-FOLD: an online resource for de novo peptide structure prediction.

1 reference

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The conformations of the amyloid-beta (21-30) fragment can be described by three families in solution

1 reference

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21 January 2018

Structures of soluble amyloid oligomers from computer simulations

1 reference

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21 January 2018

Self-assembly of amyloid-forming peptides by molecular dynamics simulations

1 reference

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Mixtures of wild-type and a pathogenic (E22G) form of Abeta40 in vitro accumulate protofibrils, including amyloid pores.

1 reference

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

1 reference

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The Alzheimer's peptides Abeta40 and 42 adopt distinct conformations in water: a combined MD / NMR study

1 reference

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Insights into stability and toxicity of amyloid-like oligomers by replica exchange molecular dynamics analyses.

1 reference

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21 January 2018

Role of the familial Dutch mutation E22Q in the folding and aggregation of the 15-28 fragment of the Alzheimer amyloid-beta protein.

1 reference

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21 January 2018

Atomic-level description of amyloid beta-dimer formation.

1 reference

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21 January 2018

Protein structure modeling with MODELLER

1 reference

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21 January 2018

GROMACS: fast, flexible, and free

1 reference

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The OPLS [optimized potentials for liquid simulations] potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin.

1 reference

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New tricks for modelers from the crystallography toolkit: the particle mesh Ewald algorithm and its use in nucleic acid simulations

1 reference

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21 January 2018

Replica-exchange molecular dynamics method for protein folding

1 reference

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21 January 2018

Molecular dynamics simulations of protein folding.

1 reference

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21 January 2018

Conformation and dynamics of a rhodamine probe attached at two sites on a protein: implications for molecular structure determination in situ

1 reference

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21 January 2018

Structural and hydration properties of the partially unfolded states of the prion protein

1 reference

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21 January 2018

Peptide folding kinetics from replica exchange molecular dynamics.

1 reference

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Simulation study of noncovalent hybridization of carbon nanotubes by single-stranded DNA in water

1 reference

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Structural basis for the interaction of isoDGR with the RGD-binding site of alphavbeta3 integrin

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Hydrogen bonding in globular proteins

1 reference

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Impact of the mutation A21G (Flemish variant) on Alzheimer's beta-amyloid dimers by molecular dynamics simulations

1 reference

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Atomic structures of amyloid cross-beta spines reveal varied steric zippers

1 reference

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21 January 2018

An amyloid-forming segment of beta2-microglobulin suggests a molecular model for the fibril

1 reference

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Annular structures as intermediates in fibril formation of Alzheimer Abeta17-42

1 reference

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Monomer adds to preformed structured oligomers of Abeta-peptides by a two-stage dock-lock mechanism.

1 reference

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Sampling the self-assembly pathways of KFFE hexamers

1 reference

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Investigating the mechanism of peptide aggregation: insights from mixed monte carlo-molecular dynamics simulations.

1 reference

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Effect of beta-sheet propensity on peptide aggregation

1 reference

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Annular protofibrils are a structurally and functionally distinct type of amyloid oligomer

1 reference

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Induced beta-barrel formation of the Alzheimer's Abeta25-35 oligomers on carbon nanotube surfaces: implication for amyloid fibril inhibition

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A single mutation in the nonamyloidogenic region of islet amyloid polypeptide greatly reduces toxicity

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Structural reorganisation and potential toxicity of oligomeric species formed during the assembly of amyloid fibrils

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New structures help the modeling of toxic amyloidbeta ion channels

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Structure of the human voltage-dependent anion channel

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A minimal transmembrane beta-barrel platform protein studied by nuclear magnetic resonance

1 reference

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Coarse-grained protein molecular dynamics simulations

1 reference

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In Silico Assembly of Alzheimer's Aβ16-22Peptide into β-Sheets

1 reference

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Self-assembly of the beta2-microglobulin NHVTLSQ peptide using a coarse-grained protein model reveals a beta-barrel species

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Thermodynamics and dynamics of amyloid peptide oligomerization are sequence dependent

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Spontaneous beta-barrel formation: an all-atom Monte Carlo study of Abeta16-22 oligomerization

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Identifiers

10.1063/1.3385470

1 reference

Europe PubMed Central

8 June 2017

1 reference

Europe PubMed Central

8 June 2017

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